ClinVar Miner

Submissions for variant NM_004273.5(CHST3):c.533dup (p.Ala179fs) (rs769540174)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Department of Medical Genetics,Sanjay Gandhi Post Graduate Institute of Medical Sciences RCV000576230 SCV000622095 pathogenic Spondyloepiphyseal dysplasia with congenital joint dislocations criteria provided, single submitter clinical testing This mutation leads to frameshift mutation (p.A179R fs*141) and was found to be pathogenic by in silico tools. Parents were found to be heterozygous carriers.
GeneDx RCV000498884 SCV000589674 likely pathogenic not provided 2017-06-12 criteria provided, single submitter clinical testing The c.533dupG variant in the CHST3 gene has been reported previously in the homozygous state, using alternate nomenclature of c.533_534insG, in two unrelated Arab individuals affected with carbohydrate sulfotransferase 3 deficiency, congenital joint dislocations, and short stature (Unger et al., 2010). The same homozygous variant was also reported in a child of Indian descent with extreme short stature, joint contractures and prominence, and vertebral abnormalities (Srivastava et al., 2017). The c.533dupG variant causes a frameshift starting with codon Alanine 179, changes this amino acid to am Arginine residue, and creates a premature Stop codon at position 141 of the new reading frame, denoted p.Ala179ArgfsX141. This variant is predicted to cause loss of normal protein function through protein truncation. The c.533dupG variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). We interpret c.533dupG as a likely pathogenic variant.

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