ClinVar Miner

Submissions for variant NM_006415.4(SPTLC1):c.397T>C (p.Cys133Arg) (rs1587953587)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001316975 SCV001507617 uncertain significance Hereditary sensory and autonomic neuropathy type 1 2020-07-26 criteria provided, single submitter clinical testing This sequence change replaces cysteine with arginine at codon 133 of the SPTLC1 protein (p.Cys133Arg). The cysteine residue is highly conserved and there is a large physicochemical difference between cysteine and arginine. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with hereditary sensory neuropathy (PMID: 19555464). ClinVar contains an entry for this variant (Variation ID: 637417). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: Deleterious; PolyPhen-2: Probably Damaging; Align-GVGD: Class C0). This variant disrupts the p.Cys133 amino acid residue in SPTLC1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 11242106, 11242114, 16364956, 18018475, 22302274, 26681808, 15546589). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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.
Inherited Neuropathy Consortium RCV000789582 SCV000928938 uncertain significance Charcot-Marie-Tooth disease no assertion criteria provided literature only

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