ClinVar Genomic variation as it relates to human health

PS3, PS4

G6PD: PM2, PS4:Moderate, PP4, PS3:Supporting

Variant summary: G6PD c.632A>T (p.Asp211Val) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00014 in 183162 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in G6PD causing Glucose 6 Phosphate Dehydrogenase Deficiency (0.00014 vs 0.29), allowing no conclusion about variant significance. c.632A>T has been reported in the literature as c.542A>T (p.Asp181Val) or G6PD Malaga in isolation and as G6PD Santamaria association with c.376A>G (p. Asn126Asp, the nondeficient polymorphic variant G6PD A+ as stated in Al-Sweedan_2012) in multiple individuals affected with clinical manifestations of Favism and Glucose 6 Phosphate Dehydrogenase Deficiency (example, Vulliamy_1996, Al Sweedan_2012, Benmansour_2013). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function in isolation and as the G6PD Santamaria haplotype (Vulliamy_1996). The most pronounced variant effect in isolation (G6PD Malaga) results in a residual RBC activity of 6.4% of normal, a slower than normal electrophoretic mobility, a markedly decreased Km for both G6P and NADP, striking decreases in utilization rates of 2-deoxy G6P and deamino NADP, a normal thermostability and pH optimum curve. The following publications have been ascertained in the context of this evaluation (PMID: 22906837, 9233561, 22963789, 8956035). ClinVar contains an entry for this variant (Variation ID: 37203). Based on the evidence outlined above, the variant in isolation and in cis with c.376A>G as G6PD Santamaria was classified as pathogenic.

Variant found in unrelated hemizygotes with deficiency, favism, and anemia (PS4_M, PP4). Decreased activity in red blood cells (6%) (PS3). Below expected carrier frequency in gnomAD (PM2). Reported as pathogenic by multiple clinical testing groups (PP5). Not found in gnomAD (PM2). Post_P 0.994 (odds of pathogenicity 1517, Prior_P 0.1).

This sequence change replaces aspartic acid, which is acidic and polar, with valine, which is neutral and non-polar, at codon 181 of the G6PD protein (p.Asp181Val). 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. The c.542A>T (p.Asp181Val) variant and the c.376A>G (p.Asn126Asp) variant, when co-occurring in cis as c.[376A>G;542A>T], is known as the G6PD Santa Maria haplotype. The c.542A>T (p.Asn181Val) variant alone (PMID: 10571945, 8956035) and the Santa Maria haplotype (PMID: 1879833, 22963789, 12367584, 8956035, 22906837) have both been observed in individuals affected with G6PD deficiency. ClinVar contains an entry for this variant (Variation ID: 37203). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on G6PD protein function. Experimental studies are not available for the c.542A>T (p.Asn181Val) variant alone, but in vitro studies have shown that the G6PD Santa Maria haplotype abrogates enzyme activity and reduces affinity for the substrate (PMID: 26633385). For these reasons, this variant has been classified as Pathogenic.

Biochemical studies of G6PD enzyme activity from patient blood samples showed that G6PD Malaga (D181V) and G6PD Santamaria (D181V+N126D) have similar abnormal kinetic properties, though G6PD Santamaria showed additional abnormalities thought to be due to the interaction of both variants (PMID: 8956035); Published functional studies demonstrate that the G6PD Santamaria variant (D181V+N126D) causes lower levels of expression of soluble protein as well as reduced enzyme activity compared to both wild-type GP6D and G6PD harboring the N126D variant alone (PMID: 26633385); In silico analysis indicates that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 27267757, 21931771, 26738565, 17611006, 10571945, 6433630, 1879833, 9233561, 8956035, 31589614, 36681081, 36007526, 34272389, 26633385, 33637102)