rs796053197
Variant summary
Our verdict is Pathogenic. Variant got 19 ACMG points: 19P and 0B. PM1PM2PM5PP2PP3_StrongPP5_Very_Strong
The NM_001040142.2(SCN2A):c.2809C>T(p.Arg937Cys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R937H) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001040142.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCN2A | NM_001040142.2 | c.2809C>T | p.Arg937Cys | missense_variant | 16/27 | ENST00000375437.7 | |
SCN2A | NM_001371246.1 | c.2809C>T | p.Arg937Cys | missense_variant | 16/27 | ENST00000631182.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCN2A | ENST00000375437.7 | c.2809C>T | p.Arg937Cys | missense_variant | 16/27 | 5 | NM_001040142.2 | P1 | |
SCN2A | ENST00000631182.3 | c.2809C>T | p.Arg937Cys | missense_variant | 16/27 | 5 | NM_001371246.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Seizures, benign familial infantile, 3;C3150987:Developmental and epileptic encephalopathy, 11 Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Mar 08, 2023 | This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 937 of the SCN2A protein (p.Arg937Cys). For these reasons, this variant has been classified as Pathogenic. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt SCN2A protein function. ClinVar contains an entry for this variant (Variation ID: 207080). This missense change has been observed in individual(s) with clinical features of SCN2A-related conditions (PMID: 23020937, 28256214, 29655203, 31332282, 31957018). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). - |
Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
Developmental and epileptic encephalopathy, 11 Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Breakthrough Genomics, Breakthrough Genomics | - | This variant was previously reported in a patient with severe non-syndromic intellectual disability [PMID: 30813884, 23020937]. Functional studies suggested the variant has destabilizing effect on the selectivity filter and affects the conductance of the channel [PMID: 30813884]. In addition, another missense variant (p.Arg937His) affecting the same codon of the identified variant has been reported as pathogenic in the context of early infantile epileptic encephalopathy 11 in the ClinVar database. - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Apr 12, 2017 | The R937C missense mutation was previously identified as a de novo variant in an individual with intellectual disability (Raunch et al., 2012). It was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The R937C variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. Additionally, this substitution alters a highly conserved residue in the predicted pore loop, between transmembrane domains 5 and 6, of the second homologous repeat domain. The variant is found in EPILEPSY panel(s). - |
Complex neurodevelopmental disorder Pathogenic:1
Pathogenic, no assertion criteria provided | provider interpretation | GenomeConnect - Simons Searchlight | Jul 02, 2018 | Submission from Simons Searchlight facilitated by GenomeConnect. Variant interpreted by the Simons Searchlight team most recently on 2018-07-02 and interpreted as Pathogenic. Variant was initially reported on 2018-03-19 by GTR ID of laboratory name 500105. The reporting laboratory might also submit to ClinVar. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at