ClinVar Miner

Submissions for variant NM_001909.5(CTSD):c.14G>C (p.Ser5Thr) (rs764386803)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000187293 SCV000240875 likely benign not specified 2015-06-19 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Invitae RCV000796035 SCV000935526 uncertain significance Neuronal ceroid lipofuscinosis 2018-11-16 criteria provided, single submitter clinical testing This sequence change replaces serine with threonine at codon 5 of the CTSD protein (p.Ser5Thr). The serine residue is weakly conserved and there is a small physicochemical difference between serine and threonine. While this variant is present in population databases (rs764386803), the frequency information is unreliable, as metrics indicate poor data quality at this position in the ExAC database. This variant has not been reported in the literature in individuals with CTSD-related disease. ClinVar contains an entry for this variant (Variation ID: 205337). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT,Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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.
Illumina Clinical Services Laboratory,Illumina RCV001103645 SCV001260436 uncertain significance Neuronal ceroid lipofuscinosis 10 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

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