ClinVar Miner

Submissions for variant NM_001365536.1(SCN9A):c.3019C>T (p.Arg1007Cys)

dbSNP: rs121908910
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000559164 SCV000649307 pathogenic Neuropathy, hereditary sensory and autonomic, type 2A; Generalized epilepsy with febrile seizures plus, type 7 2023-03-09 criteria provided, single submitter clinical testing 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 not expected to disrupt SCN9A protein function. ClinVar contains an entry for this variant (Variation ID: 6356). This missense change has been observed in individuals with autosomal dominant paroxysmal extreme pain disorder (PMID: 17145499). It has also been observed to segregate with disease in related individuals. This variant is present in population databases (rs121908910, gnomAD 0.007%). This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 996 of the SCN9A protein (p.Arg996Cys).
GeneDx RCV001559739 SCV001782030 uncertain significance not provided 2023-07-28 criteria provided, single submitter clinical testing Identified in an individual with epilepsy in published literature; however, no further clinical or segregation information was provided (Truty et al., 2019); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 34426522, 17145499, 31440721)
New York Genome Center RCV000006728 SCV002548704 uncertain significance Paroxysmal extreme pain disorder 2021-08-12 criteria provided, single submitter clinical testing
OMIM RCV000006728 SCV000026919 pathogenic Paroxysmal extreme pain disorder 2006-12-07 no assertion criteria provided literature only

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