Further phenotypical delineation of DLG3-related neurodevelopmental disorders

Further phenotypical delineation of DLG3-related neurodevelopmental disorders | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Further phenotypical delineation of DLG3-related neurodevelopmental disorders Marlène Malbos, Thierry Gautier, Amelle Shillington, Estelle Colin, and 33 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5998122/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 22 Sep, 2025 Read the published version in European Journal of Human Genetics → Version 1 posted 11 You are reading this latest preprint version Abstract SAP102, a member of the membrane-associated guanylate kinase proteins family, is a scaffolding protein encoded by the DLG3 gene whose hemizygous variants with loss-of-function effect are associated with X-linked Intellectual developmental disorder 90. We gathered international data from 17 new individuals with 16 different DLG3 variants (10 with pathogenic loss-of-function and 6 variants of uncertain significance), and reviewed genotypic and phenotypic data from 37 previously published families with 34 different variants. Using family segregation, frequency in publication databases, protein structure modelling and in silico prediction scores, we reclassified six missense variants (five from the literature and one common to our cohort and the literature) as likely benign. Among the individuals newly reported with likely pathogenic or pathogenic DLG3 variants, intellectual disability was more frequently associated with morphological features than in the literature, leading to a proposed extension of the associated X-linked intellectual developmental disorder 90 to a more syndromic neurodevelopmental disorder. In conclusion, we provide here an international clinical series of novel individuals with DLG3 variants in order to better define the clinical and molecular spectrum associated with this condition, and a review of the literature. Biological sciences/Genetics/Clinical genetics/Disease genetics Biological sciences/Genetics/Neurodevelopmental disorders DLG3 SAP102 X-linked Intellectual developmental disorder 90 loss-of-function missense Figures Figure 1 Figure 2 Introduction DLG3 encodes SAP102, a scaffolding protein member of the membrane-associated guanylate kinase protein family, which contains three PDZ, one SRC homology 3 and one guanylate kinase domains that mediate specific protein-protein interactions. SAP102 mediates glutamate receptor trafficking during synaptogenesis (1–3). This protein, which is highly expressed in the first stages of postnatal cerebral development, is found in both axons and dendrites, and is involved in synaptic function (2,3). SAP102 is predominantly expressed postsynaptically, and its absence induces a reduction in the total thalamocortical innervations of barrel cortex in mice, suggesting an important role in the thalamus (4). As for DLG3 , many of the genes involved in intellectual disability (ID) encode proteins regulating synaptic function and plasticity through an impact on the network and cognitive development (3,4). DLG3 (MIM*300189) loss-of-function variants have been involved in X-linked non-syndromic Intellectual developmental disorder 90 (MIM#300850). To date, 37 families with 34 different DLG3 variants have been reported: 18 families with 16 (likely-) pathogenic variants leading to premature stop codons (3,5–16) (nonsense, frameshift, intronic splice) and copy number variant (CNV) (17), 17 families (7,18–26) with 16 missense variants, one proband with a deep intronic variant (27), and one family with a duplication encompassing the first 18 exons out of 19 of DLG3 (size inferior to 500Kb) (28). The limited clinical history available in the literature for a majority of these cases makes it difficult to specify the developmental trajectories of affected individuals, and the pathogenicity of missense variants needs to be addressed more precisely. We present here an international clinical series of novel individuals with DLG3 variants to better define the clinical and molecular spectrum associated with this condition, and a review of the literature. Methods Between August 2022 and August 2024, individuals with a candidate DLG3 variant (single nucleotide variant, delins or CNV) were internationally recruited through GeneMatcher (29) and other collaboration calls. Clinical and molecular geneticists were contacted and offered the opportunity to include individuals in a descriptive clinical study comprising two groups: individuals with pathogenic (P) or likely pathogenic (LP) variants, and individuals with variant of uncertain significance (VUS). Clinical data was obtained through a standardized questionnaire. DLG3 variants had been identified by exome sequencing, genome sequencing, targeted genes panel or chromosomal microarray (Supplemental methods). All reported variants are reported in NM_021120.4, NP_066943.2 or are indicated in GRCh38 (gDNA). Additional RNA-analysis was carried out in some individuals. For VUS, in silico prediction scores and additional elements regarding the variant (e.g. RNA analysis) were verified prior to individual inclusion. The potential impact of missense variants was assessed by in silico structural modelling (Supplemental methods), and the clinical interest of each VUS was reevaluated using the American College of Medical Genetics and Genomics recommendations criteria (30). Individuals with variants reclassified as likely benign were not included in the clinical assessment. Results Cohort’s molecular data Data were obtained from 15 centers having identified 19 new individuals (17 families) with 17 different monoallelic variants. The 17 variants of interest included 10 P/LP variants and 7 VUS (Fig. 1 , Table 1 ). Pathogenic and likely pathogenic variants The 10 P/LP variants included out-of-frame delins (5/10), nonsense (3/10), one splice variant causing exon 8 skipping and leading to a disrupted reading frame (1/10) (Fig. 1 in Supplemental results), and one CNV deletion encompassing the last exon of DLG3 (1/10). In three out of ten individuals, the variant occurred de novo , and the other seven variants were inherited from two symptomatic and five asymptomatic mothers. In our female proband, no skewed X-inactivation was evidenced. Variants of Uncertain Significance Two brothers with ID carried the p.(Arg574Gln) missense variant. This variant had been previously reported in the literature as LP but without any functional assay in support of its deleterious effect (23). Maternal inheritance was suspected in the siblings of the cohort, but segregation could not be confirmed. We reclassified the variant as likely benign, as it is present in 18 male individuals with good data quality scores in gnomAD v4.1.0 (for molecular details and ACMG criteria, see Table 2 .a in Supplemental results). Therefore, the remaining six VUS included missense variants (3/6), a delins (1/6), an intronic splice variant (1/6), and an intragenic CNV deletion encompassing the beginning of the last exon in DLG3 (1/6), in seven different individuals. The six VUS were inherited from four asymptomatic mothers including one with low-level mosaicism (3% in the buccal swab sample), and the last two mothers were of unknown phenotypic status (Fig. 2 ). Individual 11 carried a splice (c.840 + 4A > G) variant, absent in gnomAD v4.1.0, whose in silico scores predict abolition or weakening of the DLG3 intron 5 splice donor site (SPiP: 98.41; spliceAI donor loss: 0.86). Individual 12 carried the p.(Arg385Cys) missense variant located in the PDZ-associated domain of NMDA receptors (Fig. 1 B). This variant is present in one male in gnomAD v4.1.0. Overall, in silico predictions were in favor of a deleterious effect (PolyPhen-2: 0.98, CADD: 27.6; REVEL 0.54), with no prediction of a splicing effect. In silico modelling suggested this variant would have little impact on structure and surface charge (Fig. 2 G, Table 2 .a in Supplemental results). Skewed X-inactivation (85:15) was observed in the individual’s asymptomatic carrier mother, while the variant was absent in his asymptomatic older sister. Individual 13 carried the p.(Ser491Cys) missense variant located in a region predicted to be intolerant to missense (MetaDome tolerance score: 0.27). This variant was absent in gnomAD v4.1.0. In silico predictions were conflicting (CADD: 26; polyphen-2: 0.97; REVEL (31): 0.431 uncertain), with no predicted splicing effect. In silico protein modelling suggested little structural impact (Fig. 2 G, Table 2 .a in Supplemental results). In the individual’s family, one child of his maternal grandmother’s sister was reported to have ID without further details, and segregation analysis could not be extended beyond his parents. Brothers 14 and 15 carried the p.(Arg661Trp) missense variant located in the GK domain (Fig. 1 B). This variant was absent in gnomAD v4.1.0. In silico predictions were in favor of a deleterious effect (CADD: 25.9; polyphen-2: 1; REVEL: 0.614) with no prediction of a splicing effect, and in silico modelling was in favor of a major steric clash (Fig. 2 G, Table 2 .a in Supplemental results). Individual 16 carried an intronic delins variant (c.2348-42_2348-4delinsAAGAGGAAAACAAAATTATTACTGTATACAG), for which RNA analysis showed a retention of intron 18 (data not shown). Individual 17 carried an intragenic deletion, which will be further analyzed using RNA-based analysis and short-reads next-generation sequencing. Therefore, after reanalysis, we retained 16 variants of interest affecting 17 individuals (16 families). Clinical data Individuals were predominantly males (16/17). The median age was 8 years and 1 month (2.5 to 38 years). Four adults (19 to 38 years) were included. The main clinical features are available in Table 2 ; and compared with the literature in Table 3 , and further details for individuals carrying VUS are provided in Supplemental results Table 1 . A comparison of the features from the individuals in our cohort and previously reported individuals is available in Table 3 . Pathogenic and likely pathogenic variants Of the 10 proband individuals, ID was reported in seven and suspected in the remaining three, who could not yet be formally diagnosed due to their age. All individuals had language impairment (10/10), but gross motor delay was inconsistent (7/10), the remaining three individuals corresponding to two individuals without motor delay, and one individual with a fine motor delay, who is therefore not considered to have a global developmental delay (7/10). Other neurodevelopmental disorders were present in 7/10 probands, consistent with autism spectrum disorder (ASD) (1/10), attention deficit hyperactivity disorder (ADHD) (2/10), agitation and risky behavior and/or hyperactivity without a proper diagnosis of ADHD (4/10). Neurological features included hypotonia (4/10) and epilepsy (2/10). Psychiatric disorders were reported in 4/9 individuals, and included behavioral disorders (4/9), anxiety (2/9), and psychosis (1/9). Nonspecific morphological features were noted in 8/10 individuals. Strabismus was reported in 2/10 individuals. Regarding sensory disorders, 1/8 individual presented a visual disorder (hyperopia and astigmatism), but no hearing loss was reported (0/7). Variants of Uncertain Significance Of the 7 individuals (6 families), ID was confirmed in the 4/4 individuals eligible for formal diagnosis and suspected in the 3/3 individuals not yet eligible. Language impairment and motor delay were inconsistent (5/7 and 3/7 respectively). Other neurodevelopmental disorders were present in 6/6 individuals, and included ASD (3/6), ADHD (1/6), and agitation or attention disorder without a formal diagnosis (4/6). For the neurological features, hypotonia was reported in 2/5 individuals and no epilepsy was reported (0/6). Psychiatric disorders included behavioral disorders (3/7), anxiety (2/7), and psychosis (1/7). Morphological features were reported in 4/7 individuals, while the two siblings 14 and 15 showed only one notable morphological feature (high-arched palate). Strabismus was reported in 1/6 individuals. Regarding sensory disorders, 2/6 individuals had a visual impairment (myopia, and/or astigmatism), and no hearing loss was reported (0/5). Literature A literature review identified 16 DLG3 missense variants that were originally classified as LP or VUS in 19 individuals, the majority of whom were males (16/19). A reassessment of ACMG criteria using gnomAD v4.1.0 led us to suggest the reclassification of the following missense variants to likely benign, in addition to the p.(Arg574Gln) variant also present in our cohort: p.(Gly43Val), p.(Pro84Leu), p.(Gly102Ser), p.(Arg198Gln), and p.(Ser475Leu) (see Table 4 and Table 2.b in Supplemental results for molecular details and ACMG criteria). Discussion Previous clinical descriptions of the phenotype associated with pathogenic DLG3 variants report non-syndromic ID but lack information regarding developmental trajectories. By reporting 10 novel proband individuals with 10 P/LP variants including nine previously unreported variants, we aimed to clarify developmental trajectories and provide details concerning the clinical features of individuals carrying P/LP DLG3 variants. Developmental delay and language impairment appeared as key features, since they were present in all probands (10/10). These language disorders may be partly explained by a possible effect on the hippocampus, where the gene is highly expressed in mammals (32), which involvement in memory has been suggested to play a role in language (33). Other neurodevelopmental (i.e. ASD, ADHD, and agitation and hyperactivity without a proper diagnosis) and psychiatric disorders (i.e. behavioral disorders, anxiety and psychosis) were also frequent (7/10 and 4/9, respectively), and more frequent than previous reports in the literature (Table 3). Otherwise, while DLG3 loss-of-function variants have been involved in non-syndromic ID to date, morphological features (8/10) were more frequently associated than initially suggested. Indeed, the affected individuals also presented some previously unreported features including decreased pain sensitivity, hypospadias, cleft palate and premature fontanel closure (Table 2). The frequent association of ID with other morphological features in our cohort leads us to question the OMIM classification of non-syndromic ID initially associated with DLG3 . However, it is difficult to make a clear distinction between non-syndromic and syndromic ID, and several genes located on the X-chromosome have already been associated with both forms of ID (34). Another aim of our study was to discuss the pathogenicity of DLG3 VUS, particularly missense variants, even though there is a lack of functional studies needed to clearly assert their possible pathogenicity. Regarding the potential deleterious effect of missense variants, the difference between expected and observed missense variants (gnomAD database, v2.1.1) is slightly in favor of an intolerance to DLG3 missense variants. We did not identify any region or domain that seems to be enriched in missense VUS in the cohort or the literature. We report three new remaining missense VUS (p.(Arg385Cys), p.(Ser491Cys), and p.(Arg661Trp)) in four individuals. We reclassified as likely benign one missense variant, p.(Arg574Gln), also present in the literature (Table 2.a in Supplemental results) (23). In the literature, 16 missense variants have been reported (Table 2.b in Supplemental results) (7,18–26). To assess their classification, we used in silico prediction scores, residue conservation among species, and the possible location in a functional domain and/or in an intolerant region for missense variants, exclusion of other potential candidate variants, and the presence (and frequency) in population databases. Since DLG3 is located on the X-chromosome and individuals with a DLG3 -related phenotype exhibit ID, the presence of asymptomatic males carrying a DLG3 variant in population databases was an important criterion supporting the non-deleterious effect of a variant, but the situation remained complex for female carriers. However, as the redundancy of certain criteria with in silico prediction scores may be seen as a limitation of our classification, it could be important to individually study each of them. Using these criteria, the p.(Arg574Gln) variant present both in our cohort and in the literature, and 5 other variants reported in the literature should, in our view, be reclassified as likely benign (p.(Gly43Val), p.(Pro84Leu), p.(Gly102Ser), p.(Arg198Gln), and p.(Ser475Leu)), leaving 10 missense VUS from literature (p.(His6Gln), p.(Pro155Ser), p.(Arg472His), p.(Leu496Phe), p.(Asp598Asn), p.(Arg621Trp), p.(Asn666Lys), p.(Leu701Phe), p.(Arg756Gln), and p.(Gly787Ser)). Thus, a total of 13 missense variants remained VUS, that are absent in males in the gnomAD v4.1 database, except for the p.(Arg385Cys) and the p.(Arg472His) variants, present respectively in 1 and 2 males. It seems insufficient to exclude these variants, especially considering that the individual with the p.(Arg385Cys) variant appears to have a milder neurodevelopmental disorder. In silico prediction scores of the remaining missense VUS are mostly conflicting, with the p.(Arg385Cys), the p.(Arg621Trp) and the p.(Arg661Trp) variants having overall prediction scores in favor of a deleterious effect. Transition from a hydrophilic to a hydrophobic residue according to the Fauchère and Pliska scale (35) occurred in the p.(Arg385Cys), p.(Arg621Trp), and p.(Arg661Trp) variants. Modelling evidenced a loss of hydrogen bonds for the p.(Arg472His), the p.(Asp598Asn), the p.(Asn666Lys), and the p.(Leu701Phe) variants (Table 4, Figure 2 in Supplemental results). There was structural destabilization in the p.(Arg472His), p.(Leu701Phe), and p.(Arg661Trp) variants, with modeling for the latter showing an important effect with a steric clash zone (Figure 2G). However, SAP102 stabilization at post-synaptic sites is depends on the SRC homology 3 and guanylate kinase domains (36). According to p.(Ser491Cys) variant modelling, little structural impact is expected (Figure 2G), but a disulfide bridge formation cannot be ruled out. Moreover, the p.(Arg385Cys) variant was predicted to have little impact on structure and on surface charge, but it could be sufficient to induce a perturbation of the third PDZ-domain (Figure 2G). Assuming that DLG3 missense variants were associated with a deleterious effect, the question of the mechanism would remain. The fact that missense variants could generate a loss-of-function effect was previously mentioned as a consequence of a loss of hydrogens bonds or protein stability disruption (18). Moreover, to our knowledge, no other mechanism leading to DLG3 pathogenicity has been described. The mechanism of the amplification previously reported as likely causal by Magini et al. for the phenotype (epilepsy and ID) of two individuals, and comprising KIF4A and a large part of DLG3 was uncertain (28). Loss-of-function has been evoked, primarily following a potential interruption of DLG3 , but another type of effect cannot be ruled out. However, the causal gene or potential implication of both of them was not definitively assessed. Other VUS reported in the present cohort (i.e. delins, intronic splicing variant and CNV) seem to be good candidates to explain the phenotypes of individuals 11, 16 and 17, but require more functional studies or data to be considered as causal. Individual 11 might be included in the PERSYST (Pathogenic Evaluation of Recalcitrant Variants by Systematic Transactivation) project, and further analyses are ongoing for individual 17, carrier of the CNV (RNA study, and short-read genome sequencing), which could help to eventually reclassify their variant. One limitation of this paper may be the transcript used (ENST00000374360.8-NM_021120.4), given that there are ten different transcripts for DLG3 (13). Transcript changes can significantly impact the predicted protein effect, as for the variant described by Matis et al. in one individual, which was associated with two de novo variants in KMT2A and PAX3 (27). The variant transitions from a frameshift in an alternative transcript to a deep intronic variant in the MANE transcript (NM_020730.2:c.127del p.(Asp43MetfsTer) and NM_021120.4:c.1145+722del p.? respectively), highlighting the importance of functional studies to confirm its involvement in the individual’s phenotype (27). However, only four of these transcripts are protein-coding, and two, including our transcript (but not NM_020730.2), are predominantly brain-specific and contain the first seven exons, in which several pathogenic variants have been reported (7,13–15) (Figure 1B). The MANE transcript is also the transcript most commonly used to describe previous variants in the literature. Another limitation concerns the comparison of clinical features seeing as precise clinical data were not available for all individuals reported in the literature. With regard to the involvement of DLG3 in female probands, it is interesting to note that both symptomatic and asymptomatic female individuals have been reported without skewed X-inactivation (3,5,6,11). Nevertheless, it is important to keep in mind that X-inactivation could be entirely different in the brain. In conclusion, our cohort reports 10 probands carrying P/LP DLG3 variants with ID frequently associated with neurodevelopmental or psychiatric disorders, leading to suggest an extension of the initial description of non-syndromic X-linked intellectual developmental disorder to a more syndromic neurodevelopmental disorder. Our cohort also includes seven individuals (six families) carrying VUS for which functional studies are required to help with reclassification, particularly for the three remaining missense variants. Declarations Data Availability Statement The datasets generated and analyzed during the current study are available from the corresponding author upon reasonable request Acknowledgments The authors are grateful to the probands and their families for their participation in this study. We thank the Centre de Calcul de l’Université de Bourgogne (CCuB) for the technical support and management of the informatics platform, the Centre de Ressources Biologiques Ferdinand Cabanne (CRB) of Dijon University Hospital for sample biobanking, the GeneMatcher platform for data sharing, and Suzanne Rankin (Dijon University Hospital) for reviewing the English Manuscript. Several authors are part of the European Reference Network for Developmental Anomalies and Intellectual Disability (ERN-ITHACA). Author contributions Clinical and molecular data curation: MM, AS, EC, XLG, OC, BI, BC, CM, BK, SW, CJ, TD, DC, JP, JL, XL, Alain V., TN, AJ, MPM, SM, ASDP, FTMT, ALB, CP, CTR, Antonio V., LF. Modelling analysis: TG, JG, MM. Writing original draft: MM, CTR, Antonio V., LF. Writing-review and editing: all authors. Ethical statement Data obtained in this study were collected retrospectively and anonymously. They did not require any ethical authorization according to the French law. Our establishment’s clinical research department was nevertheless consulted. Protocol for DEFIDIAG project was approved by the Ethics Committee Sud Méditerranée I and the French data privacy commission (CNIL, authorization 919361). Probands/families agreed for publication and signed a specific consent when they agreed for publishing recognizable photographs. Conflict of interest statement The authors report no commercial or financial relationships that could be construed as a potential conflict of interest. Funding Statement This work was supported by grants from the Dijon University Hospital, the European Union through the FEDER programs and the French Genomic Medicine Initiative (PFMG2025-DEFIDIAG study). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. References Elias GM, Elias LAB, Apostolides PF, Kriegstein AR, Nicoll RA. Differential trafficking of AMPA and NMDA receptors by SAP102 and PSD-95 underlies synapse development. Proc Natl Acad Sci U S A. 30 déc 2008;105(52):20953‑8. Wei Z, Behrman B, Wu WH, Chen BS. Subunit-specific Regulation of N-Methyl-d-aspartate (NMDA) Receptor Trafficking by SAP102 Protein Splice Variants. J Biol Chem. 20 févr 2015;290(8):5105‑16. Zanni G, van Esch H, Bensalem A, Saillour Y, Poirier K, Castelnau L, et al. A novel mutation in the DLG3 gene encoding the synapse-associated protein 102 (SAP102) causes non-syndromic mental retardation. Neurogenetics. 1 mai 2010;11(2):251‑5. 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Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, et al. Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. mai 2015;17(5):405‑24. Ioannidis NM, Rothstein JH, Pejaver V, Middha S, McDonnell SK, Baheti S, et al. REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants. Am J Hum Genet. 6 oct 2016;99(4):877‑85. Oliva C, Escobedo P, Astorga C, Molina C, Sierralta J. Role of the maguk protein family in synapse formation and function. Developmental Neurobiology. 2012;72(1):57‑72. Duff MC, Brown-Schmidt S. The hippocampus and the flexible use and processing of language. Front Hum Neurosci [Internet]. 5 avr 2012 [cité 9 oct 2024];6. Disponible sur: https://www.frontiersin.org/journals/human-neuroscience/articles/10.3389/fnhum.2012.00069/full Ropers HH. X-linked mental retardation: many genes for a complex disorder. Current Opinion in Genetics & Development. 1 juin 2006;16(3):260‑9. Fauchere J, Pliska V. Hydrophobic parameters II of amino acid side-chains from the partitioning of N-acetyl-amino acid amides. Eur J Med Chem. 1 janv 1983;18. Zheng CY, Petralia RS, Wang YX, Kachar B, Wenthold RJ. SAP102 Is a Highly Mobile MAGUK in Spines. J Neurosci. 31 mars 2010;30(13):4757‑66. Rodrigues CHM, Pires DEV, Ascher DB. DynaMut2: Assessing changes in stability and flexibility upon single and multiple point missense mutations. Protein Science. 2021;30(1):60‑9. Tables Tables 1 and 2 are available in the Supplementary Files section. Table 3 Comparison of the main clinical features of individuals reported in the present cohort (distributed according to their variants) and in the literature (male individuals carrying or suspected to carry their familial likely pathogenic or pathogenic non-missense DLG3 variant). Signs Present cohort: likely pathogenic/pathogenic variants Literature (likely pathogenic/ pathogenic non-missense variants) Present cohort: non-missense variants of uncertain significance Present cohort: missense variants of uncertain significance Literature (missense variants) Developmental delay (global or not) £ 10/10 (100%) NA 3/3 (100%) 2/4 π (50%) 10/17 § (59%) Global developmental delay 7/10 (70%) NA 1/3 (33%) 2/4 (50%) NA Intellectual disability (ID) 7/7 (100%) 48/48 (100%) 2/2 (100%) 2/2 (100%) 14/17 (82%) Suspicion of ID 3/3 † (100%) 3/3 (100%) 1/1 (100%) 2/2 (100%) NA Seizures 2/10 (20%) 5 (10%) 0/3 - 0/3 - 12/17 (71%) Other neurodevelopmental disorders 7/10 (70%) 4 (8%) 3/3 (100%) 3/3 (100%) 4/14 (29%) Psychiatric/ behavioral disorder 4/9 (44,4%) 7 * (15%) 1/3 (33%) 3/4 (75%) 1/14 (7%) Hypotonia 4/10 (40%) 5 (10%) 1/3 (33%) 1/3 (33%) 0/18 - Abnormal morphological features (> 1 feature) 8/10 (80%) 5 µ (11,5%) 2/3 (66%) 2/4 µ (50%) 2/18 (11%) Strabismus 2/10 (20%) 6 € (13%) 0/3 - 1/3 (33%) 0/18 - Visual impairments £ 1/8 (12,5%) NA 1/3 (33%) 1/3 (33%) 2/18 (11%) Total 10 51 (male patients) ∞ 3 4 19 £ available information was not sufficient to evaluate the accurate number of individuals presenting the clinical feature; π learning delay without motor delay was described in two individuals, who are therefore not counted as having global developmental delay; § one individual was described as having developmental delay and/or ID; † individuals who were not yet eligible for a formal diagnosis of intellectual disability (younger than 6 year-old); * including one individual described as having a difficult behavior as a child, without details; μ two individuals described in this cohort and two in the literature have only one morphological feature, and are not counted in the individuals presenting morphological features; € one individual had alternating esotropia, which resolved secondarily; ∞ a family comprising 37 male individuals with DLG3 variant and ID has been reported but clinical findings were available for only 10 of them, leading us to exclude the remaining 27 (8). Table 4 Modelling data for VUS missense from the literature. Variants (protein) DDG (initial publication) ΔΔG and PDB model used Fauchère and Pliska hydrophobicity scale Loss of bonds (initial publication when available) Modelling p.(His6Gln) -0.02Kcal/mol 1.25kcal/mol using AlphaFold model (prediction at this residue: very low confidence (34.69)) From 0.13 (neutral) to -0.22 (hydrophilic) No (hydrogen bonds) Performed by He et al. p.(Pro155Ser) -1.61Kcal/mol -0.13kcal/mol using PDB 2I1N -0.18kcal/mol using AlphaFold model (prediction at this residue: low confidence (69.79)) From 0.72 (hydrophobic) to -0.04 (slightly hydrophilic) No (hydrogen bonds) Performed by He et al. p.(Arg472His) -1.77Kcal/mol -1.47kcal/mol using our custom model* -1.22kcal/mol using AlphaFold model (prediction at this residue: confident (88.37)) From − 1.01 (hydrophilic) to 0.13 (neutral) Yes (hydrogen bonds with residue 407) Performed by He et al. p.(Leu496Phe) NA -0.5kcal/mol using our custom model* -0.69kcal/mol using AlphaFold model (prediction at this residue: very low confidence (29.14)) From 1.7 (hydrophobic) to 1.79 (hydrophobic) Yes (non-covalent hydrophobic interaction) Custom model* p.(Asp598Asn) NA 0.08kcal/mol using our custom model* 0.37kcal/mol using AlphaFold model (prediction at this residue: very low confidence (31.46)) From − 0.77 (hydrophilic) to -0.6 (hydrophilic) Yes (hydrogen bond with residue 604) Custom model* p.(Arg621Trp) NA -0.49kcal/mol using our custom model* -0.47kcal/mol using AlphaFold model (prediction at this residue: very high confidence (92.77)) From − 1.01 (hydrophilic) to 2.25 (hydrophobic) No Custom model* p.(Asn666Lys) -0.81Kcal/mol -0.08kcal/mol using our custom model* -0.07kcal/mol using AlphaFold model (prediction at this residue: very high confidence (91.73)) From − 0.6 (hydrophilic) to -0.99 (hydrophilic) Yes (hydrogen bond with residue 665) Performed by He et al. p.(Leu701Phe) NA -1.11kcal/mol using our custom model* -1.26 using AlphaFold model (prediction at this residue: very high confidence (91.06)) From 1.7 (hydrophobic) to 1.79 (hydrophobic) Yes (hydrogen bond with residue 660 and non-covalent hydrophobic interaction) Custom model* p.(Arg756Gln) NA -0.52kcal/mol using our custom model* -0.27kcal/mol using AlphaFold model (prediction at this residue: confident (77.76)) From − 1.01 (hydrophilic) to -0.22 (hydrophilic) NA Performed by Alagoz et al. p.(Gly787Ser) NA -0.45kcal/mol using our custom model* -0.64kcal/mol using AlphaFold model (prediction at this residue: very high confidence (91.29)) From 0 (neutral) to -0.04 (slightly hydrophilic) NA Performed by Alagoz et al. * this model differs from the one used for the variants of our cohort Modelling data of missense variants from the literature, including Gibbs Free Energy (ΔΔG) obtained from DynaMut2 (37) with positive score predictive of protein stabilization and negative score predictive of destabilization and effect increasing with the score, and hydrophobicity scale changes according to Fauchère and Pliska scale (35). Additional Declarations There is no duality of interest Supplementary Files SupplementalmethodsDLG3submitted.docx Supplemental methods SupplementalresultsDLG3postrelecture.docx Supplemental results Table1DLG3submitted.docx Table 1 Table2DLG3submitted.docx Table 2 Cite Share Download PDF Status: Published Journal Publication published 22 Sep, 2025 Read the published version in European Journal of Human Genetics → Version 1 posted Editorial decision: revise 22 May, 2025 Review # 2 received at journal 21 Apr, 2025 Reviewer # 3 agreed at journal 17 Apr, 2025 Reviewer # 2 agreed at journal 09 Apr, 2025 Review # 1 received at journal 17 Mar, 2025 Reviewer # 1 agreed at journal 07 Mar, 2025 Reviewers invited by journal 06 Mar, 2025 Submission checks completed at journal 26 Feb, 2025 First submitted to journal 26 Feb, 2025 Unknown event 12 Feb, 2025 Editor assigned by journal 10 Feb, 2025 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. 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13:42:42","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":43921,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cem\u003e\u003cstrong\u003eDLG3 \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003evariants in the present cohort and the literature. \u003c/strong\u003e(A) Schematic representation of the decision tree used to count and classify variants in the present cohort and in the literature (initial classification of LP/P variants by the team reporting the individual was maintained). We have chosen to separate the missense variants from the others, because it seems to us that evidences currently available are insufficient to classify them as LP/P. Each variant was only considered once in the cohort and in the literature, but one LP/P variant and one VUS are common between the literature and the cohort, which explains why there are 27 distinct LP/P variants and 19 missense variants respectively. Abbreviations: LP: likely pathogenic; P: pathogenic; VUS: variant of uncertain significance; CNV: copy number variant; LB: likely benign. (B) Schematic representation of DLG3 protein showing domains and previously reported loss-of-function variants and deletion above, and the present cohort variants below: likely pathogenic/pathogenic variants in black, and VUS in blue. Variant p.(Arg574Gln) reclassified as likely benign is not shown. Abbreviation: PDZ-ass. = PDZ-associated domain of NMDA receptors. Reference: Uniprot Q92796-Human.\u003c/p\u003e","description":"","filename":"1.png","url":"https://assets-eu.researchsquare.com/files/rs-5998122/v1/03d5d04d81fc09344d18b43b.png"},{"id":78163940,"identity":"660e788d-10d2-4757-9146-8c37493d30ce","added_by":"auto","created_at":"2025-03-10 13:42:42","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":731774,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003e(A)\u003c/strong\u003e Pedigree of individual 12 (IV.3) with the variant p.(Arg385Cys); \u003cstrong\u003e(B)\u003c/strong\u003ePedigree of individual 13 (IV.1) with the variant p.(Ser491Cys). \u003cstrong\u003e(C) \u003c/strong\u003ePictures of the individual 3 with the variant p.(Ser339LysfsTer3); \u003cstrong\u003e(D)\u003c/strong\u003e Pictures of the 7-year-old individual 5 with the variant p.(Asn45GlnfsTer44); \u003cstrong\u003e(E) \u003c/strong\u003ePictures of the 2-year-and-10-month-old individual 10 with the variant p.(Glu791Ter); \u003cstrong\u003e(F)\u003c/strong\u003e Pictures of the 4-year-old individual 13 with the variant p.(Ser491Cys). \u003cstrong\u003e(G)\u003c/strong\u003e Protein structure modelling of 4 \u003cem\u003eDLG3\u003c/em\u003e missense variants in the cohort showing the four residues involved in the missense variants of our cohort and molecular cartooning of these wild-type and mutated residues. Residues 491 and 661 are located in loops, modelling is therefore unreliable. Color coding ranges from blue (+) to red (-) to indicate the surface potential. * represents the position of the affected residue leading to structure and charge modifications. (1): Wild-type residue 385 and variant p.(Arg385Cys) showing little predicted impact on structure and on surface charge. This residue is located just before the PDZ domain, and a perturbation of the third PDZ domain could induce a deleterious effect in addition to the charge modification. (2): Wild-type residue 491 and variant p.(Ser491Cys), showing little expected structural impact. A disulfide bridge formation cannot be ruled out by modelling predictions. (3): Wild-type residue 574 and variant p.(Arg574Gln), showing a change in the surface charge protein. No interaction predicted with the third PDZ domain (data not shown). (4): Modelling showing residues from 615 to 700 including wild-type residue 661, and variant p.(Arg661Trp). Red disk represents the steric clash zone when variant creates such a dramatic effect that none of the proposed rotamers is possible without strong perturbations of the adjacent structures.\u003c/p\u003e","description":"","filename":"2.png","url":"https://assets-eu.researchsquare.com/files/rs-5998122/v1/e26f468292b026ac3ea1a5ae.png"},{"id":91954218,"identity":"296830a6-5e55-4410-bf70-b29f95e9fd25","added_by":"auto","created_at":"2025-09-23 07:06:36","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2430784,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5998122/v1/a1765179-919c-486f-9961-24ec5198b490.pdf"},{"id":78163939,"identity":"a4c84bee-44e2-42e0-b920-0849810eb3d9","added_by":"auto","created_at":"2025-03-10 13:42:42","extension":"docx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":22041,"visible":true,"origin":"","legend":"Supplemental methods","description":"","filename":"SupplementalmethodsDLG3submitted.docx","url":"https://assets-eu.researchsquare.com/files/rs-5998122/v1/1a7b9c9b23246eafbc2ae159.docx"},{"id":78163947,"identity":"ffc4f1f3-58a0-45fe-9889-575bc92c065e","added_by":"auto","created_at":"2025-03-10 13:42:42","extension":"docx","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":821546,"visible":true,"origin":"","legend":"\u003cp\u003eSupplemental results\u003c/p\u003e","description":"","filename":"SupplementalresultsDLG3postrelecture.docx","url":"https://assets-eu.researchsquare.com/files/rs-5998122/v1/3fc69f233f7d06c821f7e81d.docx"},{"id":78163945,"identity":"ed621081-c7f4-44d8-ab3f-209187ad3228","added_by":"auto","created_at":"2025-03-10 13:42:42","extension":"docx","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":24231,"visible":true,"origin":"","legend":"\u003cp\u003eTable 1\u003c/p\u003e","description":"","filename":"Table1DLG3submitted.docx","url":"https://assets-eu.researchsquare.com/files/rs-5998122/v1/e8ea55d157f820d115632bf9.docx"},{"id":78163943,"identity":"e2f0ab29-3edc-409a-833b-7e2ce197d131","added_by":"auto","created_at":"2025-03-10 13:42:42","extension":"docx","order_by":4,"title":"","display":"","copyAsset":false,"role":"supplement","size":38503,"visible":true,"origin":"","legend":"\u003cp\u003eTable 2\u003c/p\u003e","description":"","filename":"Table2DLG3submitted.docx","url":"https://assets-eu.researchsquare.com/files/rs-5998122/v1/9b96e096cc05b15f497c3c1a.docx"}],"financialInterests":"There is no duality of interest","formattedTitle":"Further phenotypical delineation of DLG3-related neurodevelopmental disorders","fulltext":[{"header":"Introduction","content":"\u003cp\u003e \u003cem\u003eDLG3\u003c/em\u003e encodes SAP102, a scaffolding protein member of the membrane-associated guanylate kinase protein family, which contains three PDZ, one SRC homology 3 and one guanylate kinase domains that mediate specific protein-protein interactions. SAP102 mediates glutamate receptor trafficking during synaptogenesis (1\u0026ndash;3). This protein, which is highly expressed in the first stages of postnatal cerebral development, is found in both axons and dendrites, and is involved in synaptic function (2,3). SAP102 is predominantly expressed postsynaptically, and its absence induces a reduction in the total thalamocortical innervations of barrel cortex in mice, suggesting an important role in the thalamus (4). As for \u003cem\u003eDLG3\u003c/em\u003e, many of the genes involved in intellectual disability (ID) encode proteins regulating synaptic function and plasticity through an impact on the network and cognitive development (3,4).\u003c/p\u003e \u003cp\u003e \u003cem\u003eDLG3\u003c/em\u003e (MIM*300189) loss-of-function variants have been involved in X-linked non-syndromic Intellectual developmental disorder 90 (MIM#300850). To date, 37 families with 34 different \u003cem\u003eDLG3\u003c/em\u003e variants have been reported: 18 families with 16 (likely-) pathogenic variants leading to premature stop codons (3,5\u0026ndash;16) (nonsense, frameshift, intronic splice) and copy number variant (CNV) (17), 17 families (7,18\u0026ndash;26) with 16 missense variants, one proband with a deep intronic variant (27), and one family with a duplication encompassing the first 18 exons out of 19 of \u003cem\u003eDLG3\u003c/em\u003e (size inferior to 500Kb) (28). The limited clinical history available in the literature for a majority of these cases makes it difficult to specify the developmental trajectories of affected individuals, and the pathogenicity of missense variants needs to be addressed more precisely.\u003c/p\u003e \u003cp\u003eWe present here an international clinical series of novel individuals with \u003cem\u003eDLG3\u003c/em\u003e variants to better define the clinical and molecular spectrum associated with this condition, and a review of the literature.\u003c/p\u003e"},{"header":"Methods","content":"\u003cp\u003eBetween August 2022 and August 2024, individuals with a candidate \u003cem\u003eDLG3\u003c/em\u003e variant (single nucleotide variant, delins or CNV) were internationally recruited through GeneMatcher (29) and other collaboration calls. Clinical and molecular geneticists were contacted and offered the opportunity to include individuals in a descriptive clinical study comprising two groups: individuals with pathogenic (P) or likely pathogenic (LP) variants, and individuals with variant of uncertain significance (VUS). Clinical data was obtained through a standardized questionnaire.\u003c/p\u003e \u003cp\u003e \u003cem\u003eDLG3\u003c/em\u003e variants had been identified by exome sequencing, genome sequencing, targeted genes panel or chromosomal microarray (Supplemental methods). All reported variants are reported in NM_021120.4, NP_066943.2 or are indicated in GRCh38 (gDNA). Additional RNA-analysis was carried out in some individuals.\u003c/p\u003e \u003cp\u003eFor VUS, \u003cem\u003ein silico\u003c/em\u003e prediction scores and additional elements regarding the variant (e.g. RNA analysis) were verified prior to individual inclusion. The potential impact of missense variants was assessed by \u003cem\u003ein silico\u003c/em\u003e structural modelling (Supplemental methods), and the clinical interest of each VUS was reevaluated using the American College of Medical Genetics and Genomics recommendations criteria (30). Individuals with variants reclassified as likely benign were not included in the clinical assessment.\u003c/p\u003e"},{"header":"Results","content":"\u003cdiv id=\"Sec4\" class=\"Section2\"\u003e \u003ch2\u003eCohort\u0026rsquo;s molecular data\u003c/h2\u003e \u003cp\u003eData were obtained from 15 centers having identified 19 new individuals (17 families) with 17 different monoallelic variants. The 17 variants of interest included 10 P/LP variants and 7 VUS (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e, Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e).\u003c/p\u003e \n\u003ch3\u003ePathogenic and likely pathogenic variants\u003c/h3\u003e\n\u003cp\u003eThe 10 P/LP variants included out-of-frame delins (5/10), nonsense (3/10), one splice variant causing exon 8 skipping and leading to a disrupted reading frame (1/10) (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e in Supplemental results), and one CNV deletion encompassing the last exon of \u003cem\u003eDLG3\u003c/em\u003e (1/10). In three out of ten individuals, the variant occurred \u003cem\u003ede novo\u003c/em\u003e, and the other seven variants were inherited from two symptomatic and five asymptomatic mothers. In our female proband, no skewed X-inactivation was evidenced.\u003c/p\u003e\n\u003ch3\u003eVariants of Uncertain Significance\u003c/h3\u003e\n\u003cp\u003eTwo brothers with ID carried the p.(Arg574Gln) missense variant. This variant had been previously reported in the literature as LP but without any functional assay in support of its deleterious effect (23). Maternal inheritance was suspected in the siblings of the cohort, but segregation could not be confirmed. We reclassified the variant as likely benign, as it is present in 18 male individuals with good data quality scores in gnomAD v4.1.0 (for molecular details and ACMG criteria, see Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e.a in Supplemental results).\u003c/p\u003e \u003cp\u003eTherefore, the remaining six VUS included missense variants (3/6), a delins (1/6), an intronic splice variant (1/6), and an intragenic CNV deletion encompassing the beginning of the last exon in \u003cem\u003eDLG3\u003c/em\u003e (1/6), in seven different individuals. The six VUS were inherited from four asymptomatic mothers including one with low-level mosaicism (3% in the buccal swab sample), and the last two mothers were of unknown phenotypic status (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eIndividual 11 carried a splice (c.840\u0026thinsp;+\u0026thinsp;4A\u0026thinsp;\u0026gt;\u0026thinsp;G) variant, absent in gnomAD v4.1.0, whose \u003cem\u003ein silico\u003c/em\u003e scores predict abolition or weakening of the \u003cem\u003eDLG3\u003c/em\u003e intron 5 splice donor site (SPiP: 98.41; spliceAI donor loss: 0.86). Individual 12 carried the p.(Arg385Cys) missense variant located in the PDZ-associated domain of NMDA receptors (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eB). This variant is present in one male in gnomAD v4.1.0. Overall, \u003cem\u003ein silico\u003c/em\u003e predictions were in favor of a deleterious effect (PolyPhen-2: 0.98, CADD: 27.6; REVEL 0.54), with no prediction of a splicing effect. \u003cem\u003eIn silico\u003c/em\u003e modelling suggested this variant would have little impact on structure and surface charge (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eG, Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e.a in Supplemental results). Skewed X-inactivation (85:15) was observed in the individual\u0026rsquo;s asymptomatic carrier mother, while the variant was absent in his asymptomatic older sister. Individual 13 carried the p.(Ser491Cys) missense variant located in a region predicted to be intolerant to missense (MetaDome tolerance score: 0.27). This variant was absent in gnomAD v4.1.0. \u003cem\u003eIn silico\u003c/em\u003e predictions were conflicting (CADD: 26; polyphen-2: 0.97; REVEL (31): 0.431 uncertain), with no predicted splicing effect. \u003cem\u003eIn silico\u003c/em\u003e protein modelling suggested little structural impact (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eG, Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e.a in Supplemental results). In the individual\u0026rsquo;s family, one child of his maternal grandmother\u0026rsquo;s sister was reported to have ID without further details, and segregation analysis could not be extended beyond his parents. Brothers 14 and 15 carried the p.(Arg661Trp) missense variant located in the GK domain (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eB). This variant was absent in gnomAD v4.1.0. \u003cem\u003eIn silico\u003c/em\u003e predictions were in favor of a deleterious effect (CADD: 25.9; polyphen-2: 1; REVEL: 0.614) with no prediction of a splicing effect, and \u003cem\u003ein silico\u003c/em\u003e modelling was in favor of a major steric clash (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eG, Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e.a in Supplemental results). Individual 16 carried an intronic delins variant (c.2348-42_2348-4delinsAAGAGGAAAACAAAATTATTACTGTATACAG), for which RNA analysis showed a retention of intron 18 (data not shown). Individual 17 carried an intragenic deletion, which will be further analyzed using RNA-based analysis and short-reads next-generation sequencing.\u003c/p\u003e \u003cp\u003eTherefore, after reanalysis, we retained 16 variants of interest affecting 17 individuals (16 families).\u003c/p\u003e\n\u003ch3\u003eClinical data\u003c/h3\u003e\n\u003cp\u003eIndividuals were predominantly males (16/17). The median age was 8 years and 1 month (2.5 to 38 years). Four adults (19 to 38 years) were included.\u003c/p\u003e \u003cp\u003eThe main clinical features are available in Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e; and compared with the literature in Table\u0026nbsp;\u003cspan refid=\"Tab3\" class=\"InternalRef\"\u003e3\u003c/span\u003e, and further details for individuals carrying VUS are provided in Supplemental results Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e. A comparison of the features from the individuals in our cohort and previously reported individuals is available in Table\u0026nbsp;\u003cspan refid=\"Tab3\" class=\"InternalRef\"\u003e3\u003c/span\u003e.\u003c/p\u003e\u003cdiv id=\"Sec8\" class=\"Section2\"\u003e \u003ch2\u003ePathogenic and likely pathogenic variants\u003c/h2\u003e \u003cp\u003eOf the 10 proband individuals, ID was reported in seven and suspected in the remaining three, who could not yet be formally diagnosed due to their age. All individuals had language impairment (10/10), but gross motor delay was inconsistent (7/10), the remaining three individuals corresponding to two individuals without motor delay, and one individual with a fine motor delay, who is therefore not considered to have a global developmental delay (7/10). Other neurodevelopmental disorders were present in 7/10 probands, consistent with autism spectrum disorder (ASD) (1/10), attention deficit hyperactivity disorder (ADHD) (2/10), agitation and risky behavior and/or hyperactivity without a proper diagnosis of ADHD (4/10). Neurological features included hypotonia (4/10) and epilepsy (2/10). Psychiatric disorders were reported in 4/9 individuals, and included behavioral disorders (4/9), anxiety (2/9), and psychosis (1/9). Nonspecific morphological features were noted in 8/10 individuals. Strabismus was reported in 2/10 individuals. Regarding sensory disorders, 1/8 individual presented a visual disorder (hyperopia and astigmatism), but no hearing loss was reported (0/7).\u003c/p\u003e \u003c/div\u003e\n\u003ch3\u003eVariants of Uncertain Significance\u003c/h3\u003e\n\u003cp\u003eOf the 7 individuals (6 families), ID was confirmed in the 4/4 individuals eligible for formal diagnosis and suspected in the 3/3 individuals not yet eligible. Language impairment and motor delay were inconsistent (5/7 and 3/7 respectively). Other neurodevelopmental disorders were present in 6/6 individuals, and included ASD (3/6), ADHD (1/6), and agitation or attention disorder without a formal diagnosis (4/6). For the neurological features, hypotonia was reported in 2/5 individuals and no epilepsy was reported (0/6). Psychiatric disorders included behavioral disorders (3/7), anxiety (2/7), and psychosis (1/7). Morphological features were reported in 4/7 individuals, while the two siblings 14 and 15 showed only one notable morphological feature (high-arched palate). Strabismus was reported in 1/6 individuals. Regarding sensory disorders, 2/6 individuals had a visual impairment (myopia, and/or astigmatism), and no hearing loss was reported (0/5).\u003c/p\u003e\n\u003cp\u003e\u003cem\u003e\u003cstrong\u003eLiterature\u003c/strong\u003e\u003c/em\u003e\u003c/p\u003e\n\u003cp\u003eA literature review identified 16 \u003cem\u003eDLG3\u003c/em\u003e missense variants that were originally classified as LP or VUS in 19 individuals, the majority of whom were males (16/19). A reassessment of ACMG criteria using gnomAD v4.1.0 led us to suggest the reclassification of the following missense variants to likely benign, in addition to the p.(Arg574Gln) variant also present in our cohort: p.(Gly43Val), p.(Pro84Leu), p.(Gly102Ser), p.(Arg198Gln), and p.(Ser475Leu) (see Table 4 and Table 2.b in Supplemental results for molecular details and ACMG criteria).\u003c/p\u003e"},{"header":"Discussion","content":"\u003cp\u003ePrevious clinical descriptions of the phenotype associated with pathogenic \u003cem\u003eDLG3\u003c/em\u003e variants report non-syndromic ID but lack information regarding developmental trajectories. By reporting 10 novel proband individuals with 10 P/LP variants including nine previously unreported variants, we aimed to clarify developmental trajectories and provide details concerning the clinical features of individuals carrying P/LP \u003cem\u003eDLG3\u003c/em\u003e variants.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eDevelopmental delay and language impairment appeared as key features, since they were present in all probands (10/10). These language disorders may be partly explained by a possible effect on the hippocampus, where the gene is highly expressed in mammals\u0026nbsp;(32), which involvement in memory has been suggested to play a role in language\u0026nbsp;(33). Other neurodevelopmental (i.e. ASD, ADHD, and agitation and hyperactivity without a proper diagnosis) and psychiatric disorders (i.e. behavioral disorders, anxiety and psychosis) were also frequent (7/10 and 4/9, respectively), and more frequent than previous reports in the literature (Table 3). Otherwise, while \u003cem\u003eDLG3\u003c/em\u003e loss-of-function variants have been involved in non-syndromic ID to date, morphological features (8/10) were more frequently associated than initially suggested. Indeed, the affected individuals also presented some previously unreported features including decreased pain sensitivity, hypospadias, cleft palate and premature fontanel closure (Table 2). The frequent association of ID with other morphological features in our cohort leads us to question the OMIM classification of non-syndromic ID initially associated with \u003cem\u003eDLG3\u003c/em\u003e. However, it is difficult to make a clear distinction between non-syndromic and syndromic ID, and several genes located on the X-chromosome have already been associated with both forms of ID\u0026nbsp;(34).\u003c/p\u003e\n\u003cp\u003eAnother aim of our study was to discuss the pathogenicity of \u003cem\u003eDLG3\u003c/em\u003e VUS, particularly missense variants, even though there is a lack of functional studies needed to clearly assert their possible pathogenicity. Regarding the potential deleterious effect of missense variants, the difference between expected and observed missense variants (gnomAD database, v2.1.1) is slightly in favor of an intolerance to \u003cem\u003eDLG3\u0026nbsp;\u003c/em\u003emissense variants.\u003cem\u003e\u0026nbsp;\u003c/em\u003eWe did not identify any region or domain that seems to be enriched in missense VUS in the cohort or the literature. We report three new remaining missense VUS (p.(Arg385Cys), p.(Ser491Cys), and p.(Arg661Trp)) in four individuals. We reclassified as likely benign one missense variant, p.(Arg574Gln), also present in the literature (Table 2.a in Supplemental results)\u0026nbsp;(23). In the literature, 16 missense variants have been reported (Table 2.b in Supplemental results)\u0026nbsp;(7,18\u0026ndash;26). To assess their classification, we used \u003cem\u003ein silico\u003c/em\u003e prediction scores, residue conservation among species, and the possible location in a functional domain and/or in an intolerant region for missense variants, exclusion of other potential candidate variants, and the presence (and frequency) in population databases. Since \u003cem\u003eDLG3\u003c/em\u003e is located on the X-chromosome and individuals with a \u003cem\u003eDLG3\u003c/em\u003e-related phenotype exhibit ID, the presence of asymptomatic males carrying a \u003cem\u003eDLG3\u003c/em\u003e variant in population databases was an important criterion supporting the non-deleterious effect of a variant, but the situation remained complex for female carriers. However, as the redundancy of certain criteria with \u003cem\u003ein silico\u003c/em\u003e prediction scores may be seen as a limitation of our classification, it could be important to individually study each of them. Using these criteria, the p.(Arg574Gln) variant present both in our cohort and in the literature, and 5 other variants reported in the literature should, in our view, be reclassified as likely benign (p.(Gly43Val), p.(Pro84Leu), p.(Gly102Ser), p.(Arg198Gln), and p.(Ser475Leu)), leaving 10 missense VUS from literature (p.(His6Gln), p.(Pro155Ser), p.(Arg472His), p.(Leu496Phe), p.(Asp598Asn), p.(Arg621Trp), p.(Asn666Lys), p.(Leu701Phe), p.(Arg756Gln), and p.(Gly787Ser)).\u003c/p\u003e\n\u003cp\u003eThus, a total of 13 missense variants remained VUS, that are absent in males in the gnomAD v4.1 database, except for the p.(Arg385Cys) and the p.(Arg472His) variants, present respectively in 1 and 2 males. It seems insufficient to exclude these variants, especially considering that the individual with the p.(Arg385Cys) variant appears to have a milder neurodevelopmental disorder. \u003cem\u003eIn silico\u003c/em\u003e prediction scores of the remaining missense VUS are mostly conflicting, with the p.(Arg385Cys), the p.(Arg621Trp) and the p.(Arg661Trp) variants having overall prediction scores in favor of a deleterious effect. Transition from a hydrophilic to a hydrophobic residue according to the Fauch\u0026egrave;re and Pliska scale\u0026nbsp;(35)\u0026nbsp;occurred in the p.(Arg385Cys), p.(Arg621Trp), and p.(Arg661Trp) variants. Modelling evidenced a loss of hydrogen bonds for the p.(Arg472His), the p.(Asp598Asn), the p.(Asn666Lys), and the p.(Leu701Phe) variants (Table 4, Figure 2 in Supplemental results). There was structural destabilization in the p.(Arg472His), p.(Leu701Phe), and p.(Arg661Trp) variants, with modeling for the latter showing an important effect with a steric clash zone (Figure 2G). However, SAP102 stabilization at post-synaptic sites is depends on the SRC homology 3 and guanylate kinase domains\u0026nbsp;(36). According to p.(Ser491Cys) variant modelling, little structural impact is expected (Figure 2G), but a disulfide bridge formation cannot be ruled out. Moreover, the p.(Arg385Cys) variant was predicted to have little impact on structure and on surface charge, but it could be sufficient to induce a perturbation of the third PDZ-domain (Figure 2G).\u003c/p\u003e\n\u003cp\u003eAssuming that\u003cem\u003e\u0026nbsp;DLG3\u0026nbsp;\u003c/em\u003emissense variants were associated with a deleterious effect, the question of the mechanism would remain. The fact that missense variants could generate a loss-of-function effect was previously mentioned as a consequence of a loss of hydrogens bonds or protein stability disruption\u0026nbsp;(18). Moreover, to our knowledge, no other mechanism leading to \u003cem\u003eDLG3\u003c/em\u003e pathogenicity has been described. The mechanism of the amplification previously reported as likely causal by Magini et al. for the phenotype (epilepsy and ID) of two individuals, and comprising \u003cem\u003eKIF4A\u003c/em\u003e and a large part of \u003cem\u003eDLG3\u003c/em\u003e was uncertain\u0026nbsp;(28). Loss-of-function has been evoked, primarily following a potential interruption of \u003cem\u003eDLG3\u003c/em\u003e, but another type of effect cannot be ruled out. However, the causal gene or potential implication of both of them was not definitively assessed.\u003c/p\u003e\n\u003cp\u003eOther VUS reported in the present cohort (i.e. delins, intronic splicing variant and CNV) seem to be good candidates to explain the phenotypes of individuals 11, 16 and 17, but require more functional studies or data to be considered as causal. Individual 11 might be included in the PERSYST (Pathogenic Evaluation of Recalcitrant Variants by Systematic Transactivation) project, and further analyses are ongoing for individual 17, carrier of the CNV (RNA study, and short-read genome sequencing), which could help to eventually reclassify their variant.\u003c/p\u003e\n\u003cp\u003eOne limitation of this paper may be the transcript used (ENST00000374360.8-NM_021120.4), given that there are ten different transcripts for \u003cem\u003eDLG3\u0026nbsp;\u003c/em\u003e(13). Transcript changes can significantly impact the predicted protein effect, as for the variant described by Matis et al. in one individual, which was associated with two \u003cem\u003ede novo\u003c/em\u003e variants in \u003cem\u003eKMT2A\u003c/em\u003e and \u003cem\u003ePAX3\u0026nbsp;\u003c/em\u003e(27). The variant transitions from a frameshift in an alternative transcript to a deep intronic variant in the MANE transcript (NM_020730.2:c.127del p.(Asp43MetfsTer) and NM_021120.4:c.1145+722del p.? respectively), highlighting the importance of functional studies to confirm its involvement in the individual\u0026rsquo;s phenotype\u0026nbsp;(27). However, only four of these transcripts are protein-coding, and two, including our transcript (but not NM_020730.2), are predominantly brain-specific and contain the first seven exons, in which several pathogenic variants have been reported\u0026nbsp;(7,13\u0026ndash;15)\u0026nbsp;(Figure 1B). The MANE transcript is also the transcript most commonly used to describe previous variants in the literature.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eAnother limitation concerns the comparison of clinical features seeing as precise clinical data were not available for all individuals reported in the literature.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eWith regard to the involvement of DLG3 in female probands, it is interesting to note that both symptomatic and asymptomatic female individuals have been reported without skewed X-inactivation\u0026nbsp;(3,5,6,11). Nevertheless, it is important to keep in mind that X-inactivation could be entirely different in the brain.\u003c/p\u003e\n\u003cp\u003eIn conclusion, our cohort reports 10 probands carrying P/LP \u003cem\u003eDLG3\u003c/em\u003e variants with ID frequently associated with neurodevelopmental or psychiatric disorders, leading to suggest an extension of the initial description of non-syndromic X-linked intellectual developmental disorder to a more syndromic neurodevelopmental disorder. Our cohort also includes seven individuals (six families) carrying VUS for which functional studies are required to help with reclassification, particularly for the three remaining missense variants. \u0026nbsp;\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eData Availability Statement\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe datasets generated and analyzed during the current study are available from the corresponding author upon reasonable request\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAcknowledgments\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors are grateful to the probands and their families for their participation in this study.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eWe thank the Centre de Calcul de l\u0026rsquo;Universit\u0026eacute; de Bourgogne (CCuB) for the technical support and management of the informatics platform, the Centre de Ressources Biologiques Ferdinand Cabanne (CRB) of Dijon University Hospital for sample biobanking, the GeneMatcher platform for data sharing, and Suzanne Rankin (Dijon University Hospital) for reviewing the English Manuscript.\u003c/p\u003e\n\u003cp\u003eSeveral authors are part of the European Reference Network for Developmental Anomalies and Intellectual Disability (ERN-ITHACA).\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthor contributions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eClinical and molecular data curation: MM, AS, EC, XLG, OC, BI, BC, CM, BK, SW, CJ, TD, DC, JP, JL, XL, Alain V., TN, AJ, MPM, SM, ASDP, FTMT, ALB, CP, CTR, Antonio V., LF.\u003c/p\u003e\n\u003cp\u003eModelling analysis: TG, JG, MM.\u003c/p\u003e\n\u003cp\u003eWriting original draft: MM, CTR, Antonio V., LF.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eWriting-review and editing: all authors.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eEthical statement\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eData obtained in this study were collected retrospectively and anonymously. They did not require any ethical authorization according to the French law. Our establishment\u0026rsquo;s clinical research department was nevertheless consulted.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eProtocol for DEFIDIAG project was approved by the Ethics Committee Sud M\u0026eacute;diterran\u0026eacute;e I and the French data privacy commission (CNIL, authorization 919361).\u003c/p\u003e\n\u003cp\u003eProbands/families agreed for publication and signed a specific consent when they agreed for publishing recognizable photographs. \u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConflict of interest statement\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors report no commercial or financial relationships that could be construed as a potential conflict of interest.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding Statement\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis work was supported by grants from the Dijon University Hospital, the European Union through the FEDER programs and the French Genomic Medicine Initiative (PFMG2025-DEFIDIAG study). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003eElias GM, Elias LAB, Apostolides PF, Kriegstein AR, Nicoll RA. Differential trafficking of AMPA and NMDA receptors by SAP102 and PSD-95 underlies synapse development. Proc Natl Acad Sci U S A. 30 d\u0026eacute;c 2008;105(52):20953‑8. \u003c/li\u003e\n\u003cli\u003eWei Z, Behrman B, Wu WH, Chen BS. Subunit-specific Regulation of N-Methyl-d-aspartate (NMDA) Receptor Trafficking by SAP102 Protein Splice Variants. J Biol Chem. 20 f\u0026eacute;vr 2015;290(8):5105‑16. \u003c/li\u003e\n\u003cli\u003eZanni G, van Esch H, Bensalem A, Saillour Y, Poirier K, Castelnau L, et al. A novel mutation in the DLG3 gene encoding the synapse-associated protein 102 (SAP102) causes non-syndromic mental retardation. 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Application of Trio-Whole Exome Sequencing in Genetic Diagnosis and Therapy in Chinese Children With Epilepsy. Front Mol Neurosci. 19 ao\u0026ucirc;t 2021;14:699574. \u003c/li\u003e\n\u003cli\u003eChen Y, Tang X, Liu L, Huang Q, Lin L, Liu G, et al. Comprehensive genome sequencing analyses identify novel gene mutations and copy number variations associated with infant developmental delay or intellectual disability (DD/ID). Genes Dis. 3 d\u0026eacute;c 2021;9(5):1166‑9. \u003c/li\u003e\n\u003cli\u003eTaşkıran EZ, Karaosmanoğlu B, Koşukcu C, \u0026Uuml;rel-Demir G, Akg\u0026uuml;n-Doğan \u0026Ouml;, Şimşek-Kiper P\u0026Ouml;, et al. Diagnostic yield of whole-exome sequencing in non-syndromic intellectual disability. Journal of Intellectual Disability Research. 2021;65(6):577‑88. \u003c/li\u003e\n\u003cli\u003eAlagoz M, Kherad N, Solgun H, Ozkılıc A, Aslan E, Bozkurt S, et al. DLG3 Impairment Caused by Missense Variants in Non-Syndromic X-Linked Mental Retardation. 2021. \u003c/li\u003e\n\u003cli\u003eBowling KM, Thompson ML, Amaral MD, Finnila CR, Hiatt SM, Engel KL, et al. Genomic diagnosis for children with intellectual disability and/or developmental delay. Genome Med. 30 mai 2017;9:43. \u003c/li\u003e\n\u003cli\u003evan der Ven AT, Johannsen J, Kort\u0026uuml;m F, Wagner M, Tsiakas K, Bierhals T, et al. Prevalence and clinical prediction of mitochondrial disorders in a large neuropediatric cohort. Clinical Genetics. 2021;100(6):766‑70. \u003c/li\u003e\n\u003cli\u003eIbarluzea N, de la Hoz AB, Villate O, Llano I, Ocio I, Mart\u0026iacute; I, et al. Targeted Next-Generation Sequencing in Patients with Suggestive X-Linked Intellectual Disability. Genes (Basel). 2 janv 2020;11(1):51. \u003c/li\u003e\n\u003cli\u003eMarinakis NM, Svingou M, Veltra D, Kekou K, Sofocleous C, Tilemis FN, et al. Phenotype-driven variant filtration strategy in exome sequencing toward a high diagnostic yield and identification of 85 novel variants in 400 patients with rare Mendelian disorders. American Journal of Medical Genetics Part A. 2021;185(8):2561‑71. \u003c/li\u003e\n\u003cli\u003eMatis T, Michaud V, Van-Gils J, Raclet V, Plaisant C, Fergelot P, et al. Triple diagnosis of Wiedemann-Steiner, Waardenburg and DLG3-related intellectual disability association found by WES: A case report. The Journal of Gene Medicine. 2020;22(8):e3197. \u003c/li\u003e\n\u003cli\u003eMagini P, Scarano E, Donati I, Sensi A, Mazzanti L, Perri A, et al. Challenges in the clinical interpretation of small de novo copy number variants in neurodevelopmental disorders. Gene. 20 juill 2019;706:162‑71. \u003c/li\u003e\n\u003cli\u003eSobreira N, Schiettecatte F, Valle D, Hamosh A. GeneMatcher: A Matching Tool for Connecting Investigators with an Interest in the Same Gene. Human Mutation. oct 2015;36(10):928‑30. \u003c/li\u003e\n\u003cli\u003eRichards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, et al. Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. mai 2015;17(5):405‑24. \u003c/li\u003e\n\u003cli\u003eIoannidis NM, Rothstein JH, Pejaver V, Middha S, McDonnell SK, Baheti S, et al. REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants. Am J Hum Genet. 6 oct 2016;99(4):877‑85. \u003c/li\u003e\n\u003cli\u003eOliva C, Escobedo P, Astorga C, Molina C, Sierralta J. Role of the maguk protein family in synapse formation and function. Developmental Neurobiology. 2012;72(1):57‑72. \u003c/li\u003e\n\u003cli\u003eDuff MC, Brown-Schmidt S. The hippocampus and the flexible use and processing of language. 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Protein Science. 2021;30(1):60‑9. \u003c/li\u003e\n\u003c/ol\u003e"},{"header":"Tables","content":"\u003cp\u003e\u003cb\u003eTables 1 and 2 are available in the Supplementary Files section.\u003c/b\u003e\u003c/p\u003e\n \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab3\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 3\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eComparison of the main clinical features of individuals reported in the present cohort (distributed according to their variants) and in the literature (male individuals carrying or suspected to carry their familial likely pathogenic or pathogenic non-missense \u003cem\u003eDLG3\u003c/em\u003e variant).\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"12\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c8\" colnum=\"8\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c9\" colnum=\"9\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c10\" colnum=\"10\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c11\" colnum=\"11\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c12\" colnum=\"12\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eSigns\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colspan=\"2\" nameend=\"c3\" namest=\"c2\"\u003e \u003cp\u003ePresent cohort: likely pathogenic/pathogenic variants\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colspan=\"2\" nameend=\"c5\" namest=\"c4\"\u003e \u003cp\u003eLiterature\u003c/p\u003e \u003cp\u003e(likely pathogenic/\u003c/p\u003e \u003cp\u003epathogenic non-missense variants)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colspan=\"2\" nameend=\"c7\" namest=\"c6\"\u003e \u003cp\u003ePresent cohort: non-missense variants of uncertain significance\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colspan=\"2\" nameend=\"c9\" namest=\"c8\"\u003e \u003cp\u003ePresent cohort: missense variants of uncertain significance\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colspan=\"3\" nameend=\"c12\" namest=\"c10\"\u003e \u003cp\u003eLiterature\u003c/p\u003e \u003cp\u003e(missense variants)\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eDevelopmental delay (global or not)\u003c/b\u003e\u003csup\u003e\u003cb\u003e\u0026pound;\u003c/b\u003e\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e10/10\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e(100%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c5\" namest=\"c4\"\u003e \u003cp\u003eNA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e3/3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e(100%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e2/4\u003csup\u003eπ\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e(50%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c11\" namest=\"c10\"\u003e \u003cp\u003e10/17\u003csup\u003e\u0026sect;\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c12\"\u003e \u003cp\u003e(59%)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eGlobal developmental delay\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e7/10\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e(70%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c5\" namest=\"c4\"\u003e \u003cp\u003eNA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1/3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e(33%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e2/4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e(50%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"3\" nameend=\"c12\" namest=\"c10\"\u003e \u003cp\u003eNA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eIntellectual disability (ID)\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e7/7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e(100%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e48/48\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e(100%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e2/2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e(100%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e2/2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e(100%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c11\" namest=\"c10\"\u003e \u003cp\u003e14/17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c12\"\u003e \u003cp\u003e(82%)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eSuspicion of ID\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e3/3\u003csup\u003e\u0026dagger;\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e(100%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e3/3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e(100%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1/1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e(100%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e2/2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e(100%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"3\" nameend=\"c12\" namest=\"c10\"\u003e \u003cp\u003eNA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eSeizures\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e2/10\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e(20%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e(10%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0/3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e0/3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c11\" namest=\"c10\"\u003e \u003cp\u003e12/17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c12\"\u003e \u003cp\u003e(71%)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eOther neurodevelopmental disorders\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e7/10\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e(70%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e(8%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e3/3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e(100%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e3/3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e(100%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c11\" namest=\"c10\"\u003e \u003cp\u003e4/14\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c12\"\u003e \u003cp\u003e(29%)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003ePsychiatric/\u003c/b\u003e\u003c/p\u003e \u003cp\u003e\u003cb\u003ebehavioral disorder\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e4/9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e(44,4%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7\u003csup\u003e*\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e(15%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1/3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e(33%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e3/4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e(75%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c11\" namest=\"c10\"\u003e \u003cp\u003e1/14\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c12\"\u003e \u003cp\u003e(7%)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eHypotonia\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e4/10\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e(40%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e(10%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1/3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e(33%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e1/3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e(33%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c10\"\u003e \u003cp\u003e0/18\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c12\" namest=\"c11\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eAbnormal morphological features\u003c/b\u003e\u003c/p\u003e \u003cp\u003e\u003cb\u003e(\u0026gt;\u0026thinsp;1 feature)\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e8/10\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e(80%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e5\u003csup\u003e\u0026micro;\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e(11,5%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e2/3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e(66%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e2/4\u003csup\u003e\u0026micro;\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e(50%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c11\" namest=\"c10\"\u003e \u003cp\u003e2/18\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c12\"\u003e \u003cp\u003e(11%)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eStrabismus\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e2/10\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e(20%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e6\u003csup\u003e\u0026euro;\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e(13%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0/3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e1/3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e(33%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c11\" namest=\"c10\"\u003e \u003cp\u003e0/18\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c12\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eVisual impairments\u003c/b\u003e\u003csup\u003e\u003cb\u003e\u0026pound;\u003c/b\u003e\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e1/8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e(12,5%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c5\" namest=\"c4\"\u003e \u003cp\u003eNA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1/3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e(33%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e1/3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c9\"\u003e \u003cp\u003e(33%)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c11\" namest=\"c10\"\u003e \u003cp\u003e2/18\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c12\"\u003e \u003cp\u003e(11%)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e\u003cb\u003eTotal\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c3\" namest=\"c2\"\u003e \u003cp\u003e10\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c5\" namest=\"c4\"\u003e \u003cp\u003e51 (male patients)\u003csup\u003e\u0026infin;\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c7\" namest=\"c6\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c9\" namest=\"c8\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"3\" nameend=\"c12\" namest=\"c10\"\u003e \u003cp\u003e19\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \n\n\u003cp\u003e\u003csup\u003e\u0026pound;\u003c/sup\u003eavailable information was not sufficient to evaluate the accurate number of individuals presenting the clinical feature; \u003csup\u003e\u0026pi;\u003c/sup\u003elearning delay without motor delay was described in two individuals, who are therefore not counted as having global developmental delay;\u0026nbsp;\u003csup\u003e\u0026sect;\u003c/sup\u003eone individual was described as having developmental delay and/or ID; \u003csup\u003e\u0026dagger;\u003c/sup\u003eindividuals who were not yet eligible for a formal diagnosis of intellectual disability (younger than 6 year-old); \u003csup\u003e*\u003c/sup\u003eincluding one individual described as having a difficult behavior as a child, without details; \u003csup\u003e\u0026mu;\u003c/sup\u003etwo individuals described in this cohort and two in the literature have only one morphological feature, and are not counted in the individuals presenting morphological features; \u003csup\u003e\u0026euro;\u003c/sup\u003eone individual had alternating esotropia, which resolved secondarily; \u003csup\u003e\u0026infin;\u003c/sup\u003ea family comprising 37 male individuals with \u003cem\u003eDLG3\u003c/em\u003e variant and ID has been reported but clinical findings were available for only 10 of them, leading us to exclude the remaining 27 (8).\u003c/p\u003e\n\u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab4\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 4\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cdiv class=\"SimplePara\"\u003eModelling data for VUS missense from the literature.\u003c/div\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"6\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cdiv class=\"SimplePara\"\u003eVariants (protein)\u003c/div\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cdiv class=\"SimplePara\"\u003eDDG (initial publication)\u003c/div\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cdiv class=\"SimplePara\"\u003eΔΔG and PDB model used\u003c/div\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cdiv class=\"SimplePara\"\u003eFauch\u0026egrave;re and Pliska hydrophobicity scale\u003c/div\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cdiv class=\"SimplePara\"\u003eLoss of bonds (initial publication when available)\u003c/div\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cdiv class=\"SimplePara\"\u003eModelling\u003c/div\u003e \u003c/th\u003e \u003c/tr\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cdiv class=\"SimplePara\"\u003ep.(His6Gln)\u003c/div\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cdiv class=\"SimplePara\"\u003e-0.02Kcal/mol\u003c/div\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cdiv class=\"SimplePara\"\u003e1.25kcal/mol using AlphaFold model (prediction at this residue: very low confidence (34.69))\u003c/div\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cdiv class=\"SimplePara\"\u003eFrom 0.13 (neutral)\u003c/div\u003e \u003cdiv class=\"SimplePara\"\u003eto -0.22 (hydrophilic)\u003c/div\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cdiv class=\"SimplePara\"\u003eNo (hydrogen bonds)\u003c/div\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cdiv class=\"SimplePara\"\u003ePerformed by He et al.\u003c/div\u003e \u003c/th\u003e \u003c/tr\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cdiv class=\"SimplePara\"\u003ep.(Pro155Ser)\u003c/div\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cdiv class=\"SimplePara\"\u003e-1.61Kcal/mol\u003c/div\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cdiv class=\"SimplePara\"\u003e-0.13kcal/mol using PDB 2I1N\u003c/div\u003e \u003cdiv class=\"SimplePara\"\u003e-0.18kcal/mol using AlphaFold model (prediction at this residue: low confidence (69.79))\u003c/div\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cdiv class=\"SimplePara\"\u003eFrom 0.72 (hydrophobic)\u003c/div\u003e \u003cdiv class=\"SimplePara\"\u003eto -0.04 (slightly hydrophilic)\u003c/div\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cdiv class=\"SimplePara\"\u003eNo (hydrogen bonds)\u003c/div\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cdiv class=\"SimplePara\"\u003ePerformed by He et al.\u003c/div\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003ep.(Arg472His)\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003e-1.77Kcal/mol\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003e-1.47kcal/mol using our custom model*\u003c/span\u003e\u003c/div\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003e-1.22kcal/mol using AlphaFold model (prediction at this residue: confident (88.37))\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eFrom \u0026minus;\u0026thinsp;1.01 (hydrophilic)\u003c/span\u003e\u003c/div\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eto 0.13 (neutral)\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eYes (hydrogen bonds with residue 407)\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003ePerformed by He et al.\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003ep.(Leu496Phe)\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eNA\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003e-0.5kcal/mol using our custom model*\u003c/span\u003e\u003c/div\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003e-0.69kcal/mol using AlphaFold model (prediction at this residue: very low confidence (29.14))\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eFrom 1.7 (hydrophobic)\u003c/span\u003e\u003c/div\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eto 1.79 (hydrophobic)\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eYes (non-covalent hydrophobic interaction)\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eCustom model*\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003ep.(Asp598Asn)\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eNA\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003e0.08kcal/mol using our custom model*\u003c/span\u003e\u003c/div\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003e0.37kcal/mol using AlphaFold model (prediction at this residue: very low confidence (31.46))\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eFrom \u0026minus;\u0026thinsp;0.77 (hydrophilic)\u003c/span\u003e\u003c/div\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eto -0.6 (hydrophilic)\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eYes (hydrogen bond with residue 604)\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eCustom model*\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003ep.(Arg621Trp)\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eNA\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003e-0.49kcal/mol using our custom model*\u003c/span\u003e\u003c/div\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003e-0.47kcal/mol using AlphaFold model (prediction at this residue: very high confidence (92.77))\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eFrom \u0026minus;\u0026thinsp;1.01 (hydrophilic)\u003c/span\u003e\u003c/div\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eto 2.25 (hydrophobic)\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eNo\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eCustom model*\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003ep.(Asn666Lys)\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003e-0.81Kcal/mol\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003e-0.08kcal/mol using our custom model*\u003c/span\u003e\u003c/div\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003e-0.07kcal/mol using AlphaFold model (prediction at this residue: very high confidence (91.73))\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eFrom \u0026minus;\u0026thinsp;0.6 (hydrophilic)\u003c/span\u003e\u003c/div\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eto -0.99 (hydrophilic)\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eYes (hydrogen bond with residue 665)\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003ePerformed by He et al.\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003ep.(Leu701Phe)\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eNA\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003e-1.11kcal/mol using our custom model*\u003c/span\u003e\u003c/div\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003e-1.26 using AlphaFold model (prediction at this residue: very high confidence (91.06))\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eFrom 1.7 (hydrophobic)\u003c/span\u003e\u003c/div\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eto 1.79 (hydrophobic)\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eYes (hydrogen bond with residue 660 and non-covalent hydrophobic interaction)\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eCustom model*\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003ep.(Arg756Gln)\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eNA\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003e-0.52kcal/mol using our custom model*\u003c/span\u003e\u003c/div\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003e-0.27kcal/mol using AlphaFold model (prediction at this residue: confident (77.76))\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eFrom \u0026minus;\u0026thinsp;1.01 (hydrophilic)\u003c/span\u003e\u003c/div\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eto -0.22 (hydrophilic)\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eNA\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003ePerformed by Alagoz et al.\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003ep.(Gly787Ser)\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eNA\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003e-0.45kcal/mol using our custom model*\u003c/span\u003e\u003c/div\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003e-0.64kcal/mol using AlphaFold model (prediction at this residue: very high confidence (91.29))\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eFrom 0 (neutral)\u003c/span\u003e\u003c/div\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eto -0.04 (slightly hydrophilic)\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003eNA\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cdiv class=\"SimplePara\"\u003e\u003cspan type=\"Bold\" class=\"Bold\" name=\"Emphasis\"\u003ePerformed by Alagoz et al.\u003c/span\u003e\u003c/div\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003ctfoot\u003e \u003ctr\u003e\u003ctd colspan=\"6\"\u003e* this model differs from the one used for the variants of our cohort\u003c/td\u003e\u003c/tr\u003e \u003c/tfoot\u003e \u003c/table\u003e\u003c/div\u003e \u003cp\u003eModelling data of missense variants from the literature, including Gibbs Free Energy (\u0026Delta;\u0026Delta;G) obtained from DynaMut2 (37) with positive score predictive of protein stabilization and negative score predictive of destabilization and effect increasing with the score, and hydrophobicity scale changes according to Fauch\u0026egrave;re and Pliska scale (35).\u003c/p\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"european-journal-of-human-genetics","isNatureJournal":false,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"ejhg","sideBox":"Learn more about [European Journal of Human Genetics](http://www.nature.com/ejhg/)","snPcode":"41431","submissionUrl":"https://mts-ejhg.nature.com/cgi-bin/main.plex","title":"European Journal of Human Genetics","twitterHandle":"@ejhg_journal","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"ejp","reportingPortfolio":"Nature AJ","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"DLG3, SAP102, X-linked Intellectual developmental disorder 90, loss-of-function, missense","lastPublishedDoi":"10.21203/rs.3.rs-5998122/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-5998122/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eSAP102, a member of the membrane-associated guanylate kinase proteins family, is a scaffolding protein encoded by the \u003cem\u003eDLG3\u003c/em\u003e gene whose hemizygous variants with loss-of-function effect are associated with X-linked Intellectual developmental disorder 90. We gathered international data from 17 new individuals with 16 different \u003cem\u003eDLG3\u003c/em\u003e variants (10 with pathogenic loss-of-function and 6 variants of uncertain significance), and reviewed genotypic and phenotypic data from 37 previously published families with 34 different variants. Using family segregation, frequency in publication databases, protein structure modelling and \u003cem\u003ein silico\u003c/em\u003e prediction scores, we reclassified six missense variants (five from the literature and one common to our cohort and the literature) as likely benign. Among the individuals newly reported with likely pathogenic or pathogenic \u003cem\u003eDLG3\u003c/em\u003e variants, intellectual disability was more frequently associated with morphological features than in the literature, leading to a proposed extension of the associated X-linked intellectual developmental disorder 90 to a more syndromic neurodevelopmental disorder. In conclusion, we provide here an international clinical series of novel individuals with \u003cem\u003eDLG3\u003c/em\u003e variants in order to better define the clinical and molecular spectrum associated with this condition, and a review of the literature.\u003c/p\u003e","manuscriptTitle":"Further phenotypical delineation of DLG3-related neurodevelopmental disorders","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-03-10 13:42:37","doi":"10.21203/rs.3.rs-5998122/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"revise","date":"2025-05-22T14:58:16+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"This content is not available.","date":"2025-04-21T19:42:21+00:00","index":2,"fulltext":"This content is not available."},{"type":"reviewerAgreed","content":"This content is not available.","date":"2025-04-17T07:03:10+00:00","index":3,"fulltext":"This content is not available."},{"type":"reviewerAgreed","content":"This content is not available.","date":"2025-04-09T17:19:37+00:00","index":2,"fulltext":"This content is not available."},{"type":"editorInvitedReview","content":"This content is not available.","date":"2025-03-17T14:44:04+00:00","index":1,"fulltext":"This content is not available."},{"type":"reviewerAgreed","content":"This content is not available.","date":"2025-03-07T12:56:26+00:00","index":1,"fulltext":"This content is not available."},{"type":"reviewersInvited","content":"","date":"2025-03-06T12:20:05+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-02-26T13:38:51+00:00","index":"","fulltext":""},{"type":"submitted","content":"European Journal of Human Genetics","date":"2025-02-26T13:32:44+00:00","index":"","fulltext":""},{"type":"checksFailed","content":"","date":"2025-02-12T12:28:33+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-02-10T10:19:03+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"european-journal-of-human-genetics","isNatureJournal":false,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"ejhg","sideBox":"Learn more about [European Journal of Human Genetics](http://www.nature.com/ejhg/)","snPcode":"41431","submissionUrl":"https://mts-ejhg.nature.com/cgi-bin/main.plex","title":"European Journal of Human Genetics","twitterHandle":"@ejhg_journal","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"ejp","reportingPortfolio":"Nature AJ","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"89a50ca8-19fb-4d9d-a1a8-74613bbe1698","owner":[],"postedDate":"March 10th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[{"id":45303887,"name":"Biological sciences/Genetics/Clinical genetics/Disease genetics"},{"id":45303888,"name":"Biological sciences/Genetics/Neurodevelopmental disorders"}],"tags":[],"updatedAt":"2025-09-23T07:06:30+00:00","versionOfRecord":{"articleIdentity":"rs-5998122","link":"https://doi.org/10.1038/s41431-025-01937-3","journal":{"identity":"european-journal-of-human-genetics","isVorOnly":false,"title":"European Journal of Human Genetics"},"publishedOn":"2025-09-22 04:00:00","publishedOnDateReadable":"September 22nd, 2025"},"versionCreatedAt":"2025-03-10 13:42:37","video":"","vorDoi":"10.1038/s41431-025-01937-3","vorDoiUrl":"https://doi.org/10.1038/s41431-025-01937-3","workflowStages":[]},"version":"v1","identity":"rs-5998122","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-5998122","identity":"rs-5998122","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}