Submissions for variant NM_001365536.1(SCN9A):c.3004G>T (p.Val1002Leu)

gnomAD frequency: 0.01322  dbSNP: rs4369876

Total submissions: 16

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Eurofins Ntd Llc (ga)	RCV000080039	SCV000111933	benign	not specified	2013-08-01	criteria provided, single submitter	clinical testing
Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center	RCV000490436	SCV000267491	uncertain significance	Primary erythromelalgia	2016-03-18	criteria provided, single submitter	reference population
PreventionGenetics, part of Exact Sciences	RCV000080039	SCV000309312	likely benign	not specified		criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000490436	SCV000418510	benign	Primary erythromelalgia	2017-04-27	criteria provided, single submitter	clinical testing	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign.
Illumina Laboratory Services, Illumina	RCV000375717	SCV000418511	benign	Small fiber neuropathy	2016-06-14	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000284177	SCV000418512	benign	Paroxysmal extreme pain disorder	2017-04-27	criteria provided, single submitter	clinical testing	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign.
Illumina Laboratory Services, Illumina	RCV000389941	SCV000418514	benign	Channelopathy-associated congenital insensitivity to pain, autosomal recessive	2017-04-27	criteria provided, single submitter	clinical testing	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign.
Labcorp Genetics (formerly Invitae), Labcorp	RCV000469131	SCV000559260	benign	Neuropathy, hereditary sensory and autonomic, type 2A; Generalized epilepsy with febrile seizures plus, type 7	2025-02-03	criteria provided, single submitter	clinical testing
Athena Diagnostics	RCV000992915	SCV001145513	benign	not provided	2018-12-13	criteria provided, single submitter	clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000992915	SCV001157147	benign	not provided	2023-11-22	criteria provided, single submitter	clinical testing
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	RCV000490436	SCV001435123	benign	Primary erythromelalgia		criteria provided, single submitter	research	The heterozygous p.Val991Leu variant in SCN9A has been identified in an individual suspected to have small fibre neuropathy (PMID: 21698661). In vitro functional studies provide some evidence that the p.Pro124Ser variant will not impact protein function (PMID: 21698661). However, these types of assays may not accurately represent biological function. This variant is classified as benign for autosomal dominant small fibre neuropathy because it has been identified in >20% of Latino chromosomes, including 340 homozygotes, by ExAC (http://gnomad.broadinstitute.org/).
GeneDx	RCV000992915	SCV001898274	benign	not provided	2018-11-08	criteria provided, single submitter	clinical testing	This variant is associated with the following publications: (PMID: 25585270, 27956748, 26284228, 27535533, 21698661)
Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan	RCV000080039	SCV005088000	benign	not specified	2024-07-15	criteria provided, single submitter	clinical testing	This variant is classified as Benign based on local population frequency. This variant was detected in 23% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 21. Only high quality variants are reported.
Genetic Services Laboratory, University of Chicago	RCV000080039	SCV000152672	likely benign	not specified		no assertion criteria provided	clinical testing	Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.
Clinical Genetics, Academic Medical Center	RCV000080039	SCV001979183	benign	not specified		no assertion criteria provided	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV000992915	SCV001979509	likely benign	not provided		no assertion criteria provided	clinical testing