ClinVar Miner

Submissions for variant NM_015295.3(SMCHD1):c.5396T>G (p.Leu1799Trp)

gnomAD frequency: 0.00001  dbSNP: rs1008517374
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000733739 SCV000861835 uncertain significance not provided 2018-06-20 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001070514 SCV001235764 uncertain significance Facioscapulohumeral muscular dystrophy 2 2020-02-15 criteria provided, single submitter clinical testing This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with SMCHD1-related conditions. ClinVar contains an entry for this variant (Variation ID: 597572). 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: "Possibly Damaging"; Align-GVGD: "Class C0"). 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. This sequence change replaces leucine with tryptophan at codon 1799 of the SMCHD1 protein (p.Leu1799Trp). The leucine residue is moderately conserved and there is a small physicochemical difference between leucine and tryptophan.
Revvity Omics, Revvity RCV000733739 SCV003821919 uncertain significance not provided 2023-11-06 criteria provided, single submitter clinical testing
Ambry Genetics RCV003258953 SCV003969567 uncertain significance Inborn genetic diseases 2023-04-12 criteria provided, single submitter clinical testing The c.5396T>G (p.L1799W) alteration is located in exon 43 (coding exon 43) of the SMCHD1 gene. This alteration results from a T to G substitution at nucleotide position 5396, causing the leucine (L) at amino acid position 1799 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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