ClinVar Miner

Submissions for variant NM_001909.5(CTSD):c.1208G>C (p.Arg403Thr)

gnomAD frequency: 0.00005  dbSNP: rs779858404
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000463026 SCV000549912 uncertain significance Neuronal ceroid lipofuscinosis 2022-07-19 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with threonine, which is neutral and polar, at codon 403 of the CTSD protein (p.Arg403Thr). This variant is present in population databases (rs779858404, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with CTSD-related conditions. ClinVar contains an entry for this variant (Variation ID: 409623). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0". The threonine 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.
Mayo Clinic Laboratories, Mayo Clinic RCV002261090 SCV002541115 uncertain significance not provided 2021-11-26 criteria provided, single submitter clinical testing
Athena Diagnostics RCV002261090 SCV005620698 uncertain significance not provided 2024-11-27 criteria provided, single submitter clinical testing Available data are insufficient to determine the clinical significance of the variant at this time. The frequency of this variant in the general population is uninformative in assessment of its pathogenicity. (http://gnomad.broadinstitute.org) Polyphen and MutationTaster predict this amino acid change may be benign.

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