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rs1050828

From SNPedia

Orientationminus
Stabilizedminus
Geno Mag Summary
(-;G) 0
(A;A) 4 G6PD deficiency
(A;G) 3 G6PD deficiency carrier
(G;-) 0
(G;G) 0 common in clinvar
ReferenceGRCh38 38.1/142
ChromosomeX
Position154536002
GeneG6PD
is asnp
is mentioned by
dbSNPrs1050828
ebirs1050828
HLIrs1050828
Exacrs1050828
Varsomers1050828
Maprs1050828
PheGenIrs1050828
hapmaprs1050828
1000 genomesrs1050828
hgdprs1050828
ensemblrs1050828
gopubmedrs1050828
geneviewrs1050828
scholarrs1050828
googlers1050828
pharmgkbrs1050828
gwascentralrs1050828
openSNPrs1050828
23andMers1050828
23andMe allrs1050828
SNP Nexus

SNPshotrs1050828
SNPdbers1050828
MSV3drs1050828
GWAS Ctlgrs1050828
GMAF0.04293
Max Magnitude4
? (A;A) (A;G) (G;G) 28
OMIM305900
DescG6PD A-
Variant0002
Relatedalso
OMIM305900
DescG6PD ASAHI
Variant0054
Relatedalso
Neighborrs1050829
Distance725




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 PharmGKB
CLNACC RCV000011075.9, RCV000011076.5, RCV000011077.5, RCV000011078.5, RCV000011079.5, RCV000011157.2, RCV000079404.6, RCV000178140.1, RCV000211231.1, RCV000224469.1,


rs1050828 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 of 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 19546473OA-icon.png]). Also, the literature suggests that there is association between the rs1050828 locus and various red blood cell traits in African Americans.


[PMID 20459687OA-icon.png] 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 21153663OA-icon.png] 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 23446634OA-icon.png] 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 23696099OA-icon.png] 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).


GET Evidence
G6PD-V98M
aa_change Val98Met
aa_change_short V98M
impact not reviewed
qualified_impact Insufficiently evaluated not reviewed
overall_frequency 0.0407488
summary



GWAS snp
PMID [PMID 23696099OA-icon.png]
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 23614351OA-icon.png] The genetic risk of acute seizures in African children with falciparum malaria.