ClinVar Miner

Submissions for variant NM_000402.4(G6PD):c.1451G>A (p.Arg484His)

gnomAD frequency: 0.00001  dbSNP: rs137852324
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Dunham Lab, University of Washington RCV002305431 SCV002599391 pathogenic Anemia, nonspherocytic hemolytic, due to G6PD deficiency 2022-08-12 criteria provided, single submitter curation Variant found in unrelated hemizygotes with deficiency and jaundice, favism, and CNSHA (PS4_M, PP4). Decreased activity in red blood cells and when expressed in E. coli (PS3). Affects same amino acid as pathogenic 454R>C (ClinVar ID 93493) (PM5). Below expected carrier frequency in gnomAD (PM2). Post_P 0.997 (odds of pathogenicity 3158, Prior_P 0.1).
Labcorp Genetics (formerly Invitae), Labcorp RCV002305431 SCV003445325 pathogenic Anemia, nonspherocytic hemolytic, due to G6PD deficiency 2022-05-05 criteria provided, single submitter clinical testing The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Arg454 amino acid residue in G6PD. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 10221015, 12497642, 16088936, 22293322, 26823837). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Experimental studies have shown that this missense change affects G6PD function (PMID: 16088936). 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 G6PD protein function. ClinVar contains an entry for this variant (Variation ID: 10379). This missense change has been observed in individual(s) with favism (PMID: 2393028, 12497642). This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 454 of the G6PD protein (p.Arg454His).
OMIM RCV000011103 SCV000031330 other G6PD ANDALUS 2017-05-24 no assertion criteria provided literature only

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