ClinVar Miner

Submissions for variant NM_003793.4(CTSF):c.1100A>G (p.Asn367Ser)

gnomAD frequency: 0.00006  dbSNP: rs201500574
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001773945 SCV001992184 uncertain significance not provided 2019-04-16 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function
Labcorp Genetics (formerly Invitae), Labcorp RCV001861081 SCV002178268 uncertain significance Neuronal ceroid lipofuscinosis 13 2022-08-10 criteria provided, single submitter clinical testing This variant has not been reported in the literature in individuals affected with CTSF-related conditions. This variant is present in population databases (rs201500574, gnomAD 0.02%). This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 367 of the CTSF protein (p.Asn367Ser). ClinVar contains an entry for this variant (Variation ID: 1305235). 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. 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 serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function.
Ambry Genetics RCV002425043 SCV002742775 likely benign Inborn genetic diseases 2022-01-26 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.

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