ClinVar Miner

Submissions for variant NM_000402.4(G6PD):c.1478G>A (p.Arg493His) (rs72554664)

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000174271 SCV000225547 pathogenic not provided 2013-05-16 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000508383 SCV000603772 pathogenic not specified 2017-02-08 criteria provided, single submitter clinical testing
Fulgent Genetics,Fulgent Genetics RCV000763201 SCV000893820 pathogenic Susceptibility to malaria; Anemia, nonspherocytic hemolytic, due to G6PD deficiency 2018-10-31 criteria provided, single submitter clinical testing
Invitae RCV000823393 SCV000964252 pathogenic Anemia, nonspherocytic hemolytic, due to G6PD deficiency 2020-01-06 criteria provided, single submitter clinical testing This sequence change replaces arginine with histidine at codon 463 of the G6PD protein (p.Arg463His). The arginine residue is moderately conserved and there is a small physicochemical difference between arginine and histidine. This variant is present in population databases (rs72554664, ExAC 0.5%). This variant has been described as a common cause of glucose-6-phosphate dehydrogenase deficiency in Southeast Asia, although it has also been reported in affected individuals from other populations (PMID: 9589612, 30315739, 17726510, 21446359, 15906717, 15223006, 20236109). ClinVar contains an entry for this variant (Variation ID: 100059). This variant is also known as Kaiping in the literature. 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: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). For these reasons, this variant has been classified as Pathogenic.
OMIM RCV000011120 SCV000031347 other G6PD KAIPING 2017-05-24 no assertion criteria provided literature only
OMIM RCV000011121 SCV000031348 other G6PD ANANT 2017-05-24 no assertion criteria provided literature only
OMIM RCV000011122 SCV000031349 other G6PD DHON 2017-05-24 no assertion criteria provided literature only
OMIM RCV000011123 SCV000031350 other G6PD PETRICH-LIKE 2017-05-24 no assertion criteria provided literature only
OMIM RCV000011124 SCV000031351 other G6PD SAPPORO-LIKE 2017-05-24 no assertion criteria provided literature only
Reproductive Health Research and Development,BGI Genomics RCV000991190 SCV001142503 pathogenic Glucose 6 phosphate dehydrogenase deficiency 2020-01-06 no assertion criteria provided curation NM_001042351.1:c.1388G>A in the G6PD gene has an allele frequency of 0.007 in East Asian subpopulation in the gnomAD database. This variant has been described as a common cause of glucose-6-phosphate dehydrogenase deficiency in Southeast Asia, although it has also been reported in affected individuals from other populations (PMID: 9589612, 30315739, 17726510, 21446359, 15906717, 15223006, 20236109). Experimental studies have shown that this missense change causes a significant reduction in enzyme activity and affinity for glucose-6-phosphate (PMID: 16607506). Pathogenic computational verdict because pathogenic predictions from DANN, DEOGEN2, FATHMM-MKL, M-CAP, MVP, MutationAssessor, MutationTaster, REVEL and SIFTT. aken together, we interprete this variant as Pathogenic/Likely pathogenic. ACMG/AMP Criteria applied: PS3; PS4; PP4.

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