ClinVar Miner

Submissions for variant NM_000187.4(HGD):c.158G>A (p.Arg53Gln)

gnomAD frequency: 0.00006  dbSNP: rs200808744
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000412076 SCV000486375 likely pathogenic Alkaptonuria 2016-05-24 criteria provided, single submitter clinical testing
Invitae RCV000412076 SCV000942825 pathogenic Alkaptonuria 2023-12-26 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 53 of the HGD protein (p.Arg53Gln). This variant is present in population databases (rs200808744, gnomAD 0.01%). This missense change has been observed in individual(s) with alkaptonuria (PMID: 25681086, 25804398; Invitae). ClinVar contains an entry for this variant (Variation ID: 370939). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt HGD protein function with a positive predictive value of 80%. For these reasons, this variant has been classified as Pathogenic.
CeGaT Center for Human Genetics Tuebingen RCV001726153 SCV001962514 likely pathogenic not provided 2021-07-01 criteria provided, single submitter clinical testing
Department Of Human Genetics, Institute Of Clinical And Translational Research, Biomedical Research Center, Slovak Academy Of Sciences RCV000412076 SCV004098926 pathogenic Alkaptonuria no assertion criteria provided research The variant was originally described in AKU patients in PMID:25804398 and PMID: 25681086. It has been submitted to the HGD gene mutation database (, DB-ID: AKU_00AKU_00152).

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