ClinVar Miner

Submissions for variant NM_004273.5(CHST3):c.475T>A (p.Phe159Ile)

gnomAD frequency: 0.00004  dbSNP: rs145538723
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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 RCV000006421 SCV000836326 uncertain significance Spondyloepiphyseal dysplasia with congenital joint dislocations 2022-07-30 criteria provided, single submitter clinical testing This sequence change replaces phenylalanine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 159 of the CHST3 protein (p.Phe159Ile). This variant is present in population databases (rs145538723, gnomAD 0.005%). This missense change has been observed in individual(s) with carbohydrate sulfotransferase 3 deficiency (PMID: 20830804). ClinVar contains an entry for this variant (Variation ID: 6049). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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.
Blueprint Genetics RCV001596932 SCV001832250 likely pathogenic not provided 2019-09-05 criteria provided, single submitter clinical testing
OMIM RCV000006421 SCV000026604 pathogenic Spondyloepiphyseal dysplasia with congenital joint dislocations 2010-10-01 no assertion criteria provided literature only

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