rs1050828
| Orientation | minus |
| Stabilized | minus |
| Geno | Mag | Summary |
|---|---|---|
| (-;G) | 0 | |
| (A;A) | 4 | G6PD deficiency; Hb1Ac value may need adjusting for diabetes diagnosis |
| (A;G) | 3 | G6PD deficiency carrier; Hb1Ac value may need adjusting for diabetes diagnosis |
| (G;-) | 0 | |
| (G;G) | 0 | common in clinvar |
| Reference | GRCh38 38.1/142 |
| Chromosome | X |
| Position | 154536002 |
| Gene | G6PD |
| is a | snp |
| is | mentioned by |
| dbSNP | rs1050828 |
| dbSNP (classic) | rs1050828 |
| ClinGen | rs1050828 |
| ebi | rs1050828 |
| HLI | rs1050828 |
| Exac | rs1050828 |
| Gnomad | rs1050828 |
| Varsome | rs1050828 |
| LitVar | rs1050828 |
| Map | rs1050828 |
| PheGenI | rs1050828 |
| Biobank | rs1050828 |
| 1000 genomes | rs1050828 |
| hgdp | rs1050828 |
| ensembl | rs1050828 |
| geneview | rs1050828 |
| scholar | rs1050828 |
| rs1050828 | |
| pharmgkb | rs1050828 |
| gwascentral | rs1050828 |
| openSNP | rs1050828 |
| 23andMe | rs1050828 |
| SNPshot | rs1050828 |
| SNPdbe | rs1050828 |
| MSV3d | rs1050828 |
| GWAS Ctlg | rs1050828 |
| GMAF | 0.04293 |
| Max Magnitude | 4 |
rs1050828, also known as c.292G>A, p.Val98Met and V98M as well as the G6PD A- mutation, is a SNP residing in the G6PD gene and is located the X chromosome. G6PD codes for the enzyme glucose-6-phosphate dehydrogenase, which helps protect the cell from oxidative damage. Depending on genotype, an individual may possess one or two primary versions of the G6PD gene; type A and type B. Type A is predominantly found in people who have African ancestry.
Mutations of G6PD can cause varying degrees of G6PD deficiency, which is a disease affecting red blood cells. For example, an G to A substitution mutation at the rs1050828 (also referred to as G202A) is associated with a reduction of G6PD. The G6PD deficient genotype A- (~8-20% reduction of G6PD) is typically defined by the possession of the rs1050828 A allele (rs1050828(A;A)). In addition, individuals who are type A- almost always possess the rs1050829 G allele. G6PD deficiency frequency is highest in malarial regions where G6PD deficient individuals are typically less affected by malarial infection ([PMID 19546473
]). Also, the literature suggests that there is association between the rs1050828 locus and various red blood cell traits in African Americans.
A 2019 publication reports that this variant also has the effect of lowering HbA1c values by ~0.88%-units in hemizygous men and 0.34%-units in heterozygous women. The authors suggest that when using Hb1Ac values to diagnose type-2 diabetes, those units should be added to the measured Hb1Ac level, and a diagnosis should then be made if the sum is >6.5% (the standard diagnostic threshold).[PMID 31564435]
| ? | (A;A) (A;G) (G;G) | 28 |
|---|---|---|
|
| ||
| ClinVar | |
|---|---|
| Risk | Rs1050828(A;A) |
| Alt | Rs1050828(A;A) |
| Reference | Rs1050828(G;G) |
| Significance | Other |
| Disease | Glucose 6 phosphate dehydrogenase deficiency G6PD BETICA G6PD CASTILLA G6PD DISTRITO FEDERAL G6PD TEPIC G6PD ASAHI Anemia Favism chlorproguanil and dapsone response - Toxicity/ADR not provided |
| Variation | info |
| Gene | G6PD |
| CLNDBN | Glucose 6 phosphate dehydrogenase deficiency G6PD BETICA G6PD CASTILLA G6PD DISTRITO FEDERAL G6PD TEPIC G6PD ASAHI Anemia, nonspherocytic hemolytic, due to G6PD deficiency Favism, susceptibility to chlorproguanil and dapsone response - Toxicity/ADR not provided |
| Reversed | 1 |
| HGVS | NC_000023.10:g.153764217C>T |
| CLNSRC | HGMD OMIM Allelic Variant PharmGKB Clinical Annotation |
| CLNACC | RCV000011075.12, RCV000011076.7, RCV000011077.7, RCV000011078.7, RCV000011079.7, RCV000011157.2, RCV000079404.6, RCV000178140.1, RCV000211231.1, RCV000224469.1, |
[PMID 20459687] A total of 72 SNPs were genotyped in two populations in eastern Sudan (Hausa and Massalit),
as well as, a cohort of malaria hospital patients and a control sample set (n=449). The study found that in comparison to controls (n=69), Massalit individuals (n=60) who possess the rs105828 A allele were less susceptible to malarial infection (P=0.04).
[PMID 21153663] Study surveyed 49,094 SNPs (covering ~2,100 candidate genes)in Caucasian (n=23,439) and African American (n=7,112) individuals from five different population cohorts. Genome wide association results include that rs1050828 A allele found in African American individuals is strongly associated with certain erythrocyte phenotypes including; lower red blood cell, hemoglobin and hematocrit counts (all p values <2.0 x 10 -13).
[PMID 23446634] In order to identify SNPs associated with different red blood cell phenotypic traits a genome-wide association study was conducted on African Americans (n=16,500). The SNP rs1050828 was found to be associated with hemoglobin (Hgb), hematocrit (Hct), mean corpuscular volume (MCV), and RBC count.
[PMID 23696099] A cohort of African American medical patients (n=1904) was analyzed in a genome-wide association study where loci were correlated with certain red blood cell traits. The rs1050828 locus is associated with RBC count (P=4x10-13), mean corpuscular volume (P=1x10-14), and mean corpuscular hemoglobin (P=9x10-9).
| GWAS snp | |
|---|---|
| PMID | [PMID 23696099]
|
| Trait | Red blood cell traits |
| Title | Genetic variants that confer resistance to malaria are associated with red blood cell traits in African-Americans: an electronic medical record-based genome-wide association study. |
| Risk Allele | A |
| P-val | 4E-13 |
| Odds Ratio | .20 [0.14-0.26] x10^12/L decrease |
[PMID 23614351] The genetic risk of acute seizures in African children with falciparum malaria.
