ClinVar Miner

Submissions for variant NM_004385.5(VCAN):c.7966A>G (p.Thr2656Ala)

gnomAD frequency: 0.00014  dbSNP: rs756823982
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000349873 SCV000458759 likely benign Wagner syndrome 2016-06-14 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000349873 SCV000458760 likely benign Wagner syndrome 2016-06-14 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000295764 SCV000458761 benign Vitreoretinopathy 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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Labcorp Genetics (formerly Invitae), Labcorp RCV001850875 SCV002262434 uncertain significance not provided 2022-10-13 criteria provided, single submitter clinical testing 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 alanine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 354451). This variant has not been reported in the literature in individuals affected with VCAN-related conditions. This variant is present in population databases (rs756823982, gnomAD 0.03%). This sequence change replaces threonine, which is neutral and polar, with alanine, which is neutral and non-polar, at codon 2656 of the VCAN protein (p.Thr2656Ala).
Ambry Genetics RCV004686582 SCV005179519 uncertain significance Inborn genetic diseases 2024-05-14 criteria provided, single submitter clinical testing The c.7966A>G (p.T2656A) alteration is located in exon 8 (coding exon 7) of the VCAN gene. This alteration results from a A to G substitution at nucleotide position 7966, causing the threonine (T) at amino acid position 2656 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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