ClinVar Genomic variation as it relates to human health

This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].

A published functional study demonstrates that N126D affects the catalytic efficiency of the enzyme and affects the overall stability of the protein when compared to wild-type G6PD (Gomez-Manzo et al., 2015); A published functional study demonstrates N126D alone showed similar catalytic activity and structural stability compared to wildtype while N126D in combination with other mutations resulted in protein structural instability and reduced catalytic activity, suggesting that the additional mutations contribute to reduced enzyme activity (Praoparotai et al., 2020); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 3446582, 27535533, 23144702, 2572288, 33637102, 22307442, 21931771, 1889820, 8733135, 12524354, 9452072, 21479984, 1303173, 25201310, 2836867, 3393536, 27884173, 28195434, 26990548, 27853304, 29141760, 30161219, 29072585, 32387609, 30577886, 34272389, 34426522, 33072997, 33587123, 28902532, 28939159, 34992599, 26633385)

PS3, PS4

G6PD: PM5, PS3:Moderate, PS4:Moderate, PP1, BP4

Variant summary: G6PD c.466A>G (p.Asn156Asp) results in a conservative amino acid change located in the NAD-binding domain (IPR022674) of the encoded protein sequence. Five of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.026 in 183378 control chromosomes, predominantly at a frequency of 0.32 within the African or African-American subpopulation in the gnomAD database, including 532 homozygous females and 952 hemizygous males. The observed variant frequency within African or African-American control individuals in the gnomAD database is higher than the estimated maximal expected allele frequency for a pathogenic variant in G6PD causing Glucose 6 Phosphate Dehydrogenase Deficiency phenotype (0.29). These findings strongly suggest that the variant is a benign polymorphism found primarily in populations of African or African-American origin. c.466A>G has been reported in the literature in multiple individuals affected with G6PD Deficiency, however in most of these cases as part of a complex allele with another pathogenic variant, such as c.1058T>C (known as G6PD-Betica or G6PD-Betica Selma), c.292G>A (known as G6PD A-), or c.632A>T (known as G6PD-Santamaria) (e.g. Vulliamy_1988, Beutler_1989, Vulliamy_1996, Djigo_2019). These reports do not provide unequivocal conclusions about association of the variant with disease, as the variant was not identified in isolation in affected individuals. Several publications report experimental evidence evaluating an impact on protein function. The variant, c.466A>G, has been reported to have reduced affinity for substrate molecules compared to wild-type (e.g. Ramirez-Nava_2017), but retains approximately 70-85% of wild-type enzyme activity levels (e.g. Vulliamy_1988). The following publications have been ascertained in the context of this evaluation (PMID: 2572288, 3393536, 31525211, 29072585, 8956035, 35606495). ClinVar contains an entry for this variant (Variation ID: 100055). Based on the evidence outlined above, the variant was classified as likely benign.

The c.376A>G (p.Asn126Asp) missense variant is recognized as a disease-causing variant in the G6PD gene. Functional studies demonstrate reduced enzymatic activity of the G allele compared to WT. The prevalence of the variant in affected individuals (homozygous) is increased compared with the prevalence in controls and there is familial co-segregation with disease (Bwayo et al. 2013; Manjurano et al. 2012; Maiga et al. 2014; Shah et al. 2014; Pisani et al. 2012; Vulliamy et al. 1988; Odievre et al. 2011). This variant is has been classified as pathogenic by multiple reputable clinical testing laboratories (Emory, Division of Human Genetics at Children’s Hospital of Philadelphia). Although the frequency of this variant in the African population within ExAC (http://exac.broadinstitute.org) is high it is consistent with observed and expected based on disease incidence (31.700%). In summary, this variant c.3766A>G (p.Asn126Asp) meets our criteria for a Pathogenic classification. We have confirmed this finding in our laboratory using Sanger sequencing.

G6PD c.292G>A (p.V98M) and c.466A>G (p.N156D), often occur together in cis as part of a haplotype, referred to as the enzyme variant A- (PMID: 5448; 1303173). This variant is associated with glucose-6-phosphate dehydrogenase deficiency.

This sequence change replaces asparagine with aspartic acid at codon 126 of the G6PD protein (p.Asn126Asp). The asparagine residue is moderately conserved and there is a small physicochemical difference between asparagine and aspartic acid. This variant is the A+ (also known as A or A*) haplotype and it is present in population databases (rs1050829, ExAC 32%), being by far the most prevalent in the African subpopulation (PMID: 1303173). ClinVar contains an entry for this variant (Variation ID: 100055). In addition, the c.202G>A (p.Val68Met) variant and the c.376A>G (p.Asn126Asp) variant, when co-occurring in cis c.[202G>A;376A>G], is known as the G6PD A- haplotype which is present in the African populations at 0.2% (PMID: 2572288, 4359638). This variant alone has been reported to be non-deficient and not causative of disease (PMID: 26633385, 9858856, 8611726, 2321910, 1303173, 12737938). However, it has been reported in two individuals affected with drug-induced acute hemolytic anemia who were negative for the p.Val68Met variant, but these individuals could have another G6PD variant that is responsible for the observed phenotype (PMID: 27287612). ClinVar contains an entry for the G6PD A- haplotype (Variation ID: 10361). While this variant alone has been shown to have only a mild affect on enzyme activity, the c.[202G>A;376A>G] changes of the G6PD A- haplotype have been reported to act synergistically to cause dramatic reduction of the stability and enzymatic activity of the G6PD protein (PMID: 3393536, 1303173, 10734064, 6015571, 2836867, 16356170). For these reasons, this allele has been classified as Uncertain Significance.

The p.Asn126Asp variant, sometimes called p.Asn156Asp due to a difference in cDNA numbering, in G6PD has been reported as a polymorphism in African individuals in the literature with an allele frequency of 25% in some populations (PMID: 3393536). In vitro functional studies provide some evidence that the p.Asn126Asp variant will not impact protein function (PMID: 3393536). However, these types of assays may not accurately represent biological function. This variant has also been reported in >30% of African chromosomes, 613 hemizygotes, and 354 homozygotes by ExAC (http://gnomad.broadinstitute.org/). In summary, this variant meets criteria to be classified as benign for glucose-6-phosphate dehydrogenase deficiency.

This variant was identified as hemizygous and together with NM_001042351.3:c.202G>A._x000D_ Criteria applied: PS4, PS3_MOD, PM5_SUP

Variant found in hemizygotes with deficiency, some with anemia (PP4), but also without deficiency (BS2). Decreased activity in red blood cells (28-90%) in some hemizygotes (PS3), but normal in others (BS3). Frequency of 9.1% in gnomAD3 (BA1).

The c.376A>G (p.N126D) alteration is located in exon 5 (coding exon 4) of the G6PD gene. This alteration results from a A to G substitution at nucleotide position 376, causing the asparagine (N) at amino acid position 126 to be replaced by an aspartic acid (D). Based on the available evidence, this alteration is classified as pathogenic.

The heterozygous variant (c.376A>G; p.Asn126Asp) has been previously published by itself under the name of “A variant”; the resulting enzymatic activity of this variant was at 84% of wild type. This variant have been previously published as part of the same haplotype (A- variant) which results in reduced enzymatic activity to 10-23% of normal activity.

The G6PD p.N126D variant was identified in literature and is commonly known as the A+ allele. When the p.N126D variant is found on the same allele as the G6PD p.V68M variant it is known as the A- allele, and is one of the most common causes G6PD deficiency in the African population (Beutler_1989_PMID:2572288; Clark_2009_PMID:19223928). The variant was identified in dbSNP (ID: rs1050829) and ClinVar (classified as pathogenic by the Center for Pediatric Genomic Medicine, Mendelics, Knight Diagnostic Laboratories, Children's Hospital of Philadelphia and King Abdulaziz Medical City, classified as uncertain significance by GeneDx, BluePrint Genetics and Invitae, classified as likely benign by ARUP Laboratories and Illumina and classified as benign by the Derpatment of Genetics, Qaboos University Hospital Oman). The variant was identified in control databases in 6586 of 205081 chromosomes (722 homozygous; 1760 hemizygous) at a frequency of 0.03211 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: African in 6025 of 18923 chromosomes (freq: 0.3184), Latino in 417 of 28037 chromosomes (freq: 0.01487), Other in 68 of 5335 chromosomes (freq: 0.01275), South Asian in 14 of 19079 chromosomes (freq: 0.000734), European (non-Finnish) in 61 of 92560 chromosomes (freq: 0.000659) and Ashkenazi Jewish in 1 of 7669 chromosomes (freq: 0.00013), but was not observed in the East Asian or European (Finnish) populations. The p.Asn156 residue is conserved in mammals but not in more distantly related organisms however computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. Functional studies of the A+ allele (p.N126D variant alone), the p.V68M variant alone, and the A- allele (p.N126D + p.V68M) have demonstrated that the variants alone only cause a slight decrease in activity and enzyme yield, but show significantly decreased activity and enzyme yield when found on the same allele (A-), demonstrating a synergistic effect; therefore the A+ allele on its own is not enough to cause G6PD deficiency (Town_1992_PMID:1303173; Vulliamy_1988_PMID:3393536). In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

Variant interpreted as Uncertain significance and reported on 10-30-2020 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.