ClinVar Miner

Submissions for variant NM_006514.4(SCN10A):c.4849G>T (p.Val1617Phe)

gnomAD frequency: 0.00015  dbSNP: rs375940680
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001704586 SCV000565522 uncertain significance not provided 2024-10-17 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function
Phosphorus, Inc. RCV000577983 SCV000679918 uncertain significance Brugada syndrome 2017-08-01 criteria provided, single submitter clinical testing
Phosphorus, Inc. RCV000578045 SCV000679919 uncertain significance Hereditary sodium channelopathy-related small fibers neuropathy 2017-08-01 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000577983 SCV000819745 uncertain significance Brugada syndrome 2023-11-27 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 1617 of the SCN10A protein (p.Val1617Phe). This variant is present in population databases (rs375940680, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with SCN10A-related conditions. ClinVar contains an entry for this variant (Variation ID: 418471). 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 SCN10A protein function with a negative predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
CeGaT Center for Human Genetics Tuebingen RCV001704586 SCV002544788 uncertain significance not provided 2022-06-01 criteria provided, single submitter clinical testing
Ambry Genetics RCV002341126 SCV002634860 likely benign Cardiovascular phenotype 2020-02-14 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Fulgent Genetics, Fulgent Genetics RCV002496851 SCV002816726 uncertain significance Episodic pain syndrome, familial, 2 2021-09-06 criteria provided, single submitter clinical testing

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