ClinVar Miner

Submissions for variant NM_001136191.3(KANK2):c.1138C>T (p.Arg380Cys)

gnomAD frequency: 0.00051  dbSNP: rs144821191
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002011521 SCV002301705 uncertain significance not provided 2022-09-07 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 380 of the KANK2 protein (p.Arg380Cys). This variant is present in population databases (rs144821191, gnomAD 0.08%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with KANK2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1510116). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The cysteine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.
Fulgent Genetics, Fulgent Genetics RCV002486685 SCV002799702 uncertain significance Wooly hair-palmoplantar keratoderma syndrome; Nephrotic syndrome 16 2022-03-11 criteria provided, single submitter clinical testing
Ambry Genetics RCV004046661 SCV004889073 likely benign not specified 2022-04-12 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
PreventionGenetics, part of Exact Sciences RCV003948870 SCV004771077 uncertain significance KANK2-related disorder 2023-12-29 no assertion criteria provided clinical testing The KANK2 c.1138C>T variant is predicted to result in the amino acid substitution p.Arg380Cys. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.089% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/19-11303618-G-A). Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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