ClinVar Miner

Submissions for variant NM_198586.3(NHLRC1):c.478T>C (p.Cys160Arg) (rs200595273)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000188213 SCV000241820 uncertain significance not provided 2017-03-16 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the NHLRC1 gene. The C160R variant has been reported previously in an individual with Lafora disease; however, a second NHLRC1 variant was not detected, and staining failed to detect Lafora inclusion bodies (Singh et al., 2005). The C160R variant is observed in 20/8582 (0.2%) alleles from individuals of East Asian background (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The C160R variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. However, this substitution occurs at a position that is not conserved. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Invitae RCV001078586 SCV000759833 likely benign Lafora disease 2019-12-31 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001078586 SCV001314270 uncertain significance Lafora disease 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). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

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