ClinVar Miner

Submissions for variant NM_001365536.1(SCN9A):c.4495C>T (p.Arg1499Ter) (rs187558439)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000236436 SCV000292931 pathogenic not provided 2015-06-05 criteria provided, single submitter clinical testing The R1488X pathogenic variant in the SCN9A gene has been reported previously in a patient with CIP who was homozygous for the variant (Goldberg et al., 2007; Young et al., 2008). This pathogenic variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. R1488X was not observed in approximately 6,400 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations.
Invitae RCV000697878 SCV000826511 pathogenic Hereditary sensory and autonomic neuropathy type IIA; Generalized epilepsy with febrile seizures plus, type 7 2020-03-31 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg1488*) in the SCN9A gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs187558439, ExAC 0.01%). This variant has been reported as homozygous in an individual affected with congenital indifference to pain (PMID:17470132). ClinVar contains an entry for this variant (Variation ID: 245799) Loss-of-function variants in SCN9A are known to cause autosomal recessive SCN9A-related disorders (PMID: 17470132, 19304393). For these reasons, this variant has been classified as Pathogenic.

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