Submissions for variant NM_000402.4(G6PD):c.466A>G (p.Asn156Asp)

gnomAD frequency: 0.08672  dbSNP: rs1050829

Total submissions: 28

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	RCV000079405	SCV000280712	pathogenic	not provided	2015-08-24	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000307631	SCV000482076	likely benign	G6PD deficiency	2016-06-14	criteria provided, single submitter	clinical testing
Knight Diagnostic Laboratories, Oregon Health and Sciences University	RCV000178823	SCV000494243	pathogenic	Anemia, nonspherocytic hemolytic, due to G6PD deficiency	2016-06-28	criteria provided, single submitter	clinical testing	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.
GeneDx	RCV000079405	SCV000577148	uncertain significance	not provided	2022-11-30	criteria provided, single submitter	clinical testing	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)
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000079405	SCV000603767	likely benign	not provided	2023-11-28	criteria provided, single submitter	clinical testing
Invitae	RCV000178823	SCV000647801	uncertain significance	Anemia, nonspherocytic hemolytic, due to G6PD deficiency	2020-01-03	criteria provided, single submitter	clinical testing	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.
Blueprint Genetics	RCV000079405	SCV000928035	uncertain significance	not provided	2018-11-02	criteria provided, single submitter	clinical testing
Mendelics	RCV000178823	SCV001142113	pathogenic	Anemia, nonspherocytic hemolytic, due to G6PD deficiency	2019-05-28	criteria provided, single submitter	clinical testing
UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill	RCV001095678	SCV001251451	pathogenic	G6PD deficiency; Anemia, nonspherocytic hemolytic, due to G6PD deficiency		criteria provided, single submitter	research	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.
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	RCV000178823	SCV001435245	benign	Anemia, nonspherocytic hemolytic, due to G6PD deficiency		criteria provided, single submitter	research	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.
Ambry Genetics	RCV001267359	SCV001445540	pathogenic	Inborn genetic diseases	2023-11-20	criteria provided, single submitter	clinical testing	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.
Baylor Genetics	RCV000178823	SCV001482574	pathogenic	Anemia, nonspherocytic hemolytic, due to G6PD deficiency	2019-07-27	criteria provided, single submitter	clinical testing	This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000999876	SCV001572469	likely benign	not specified	2021-04-08	criteria provided, single submitter	clinical testing	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. 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). 15 other clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Multiple laboratories reported the variant with conflicting assessments (benign/likely benign, n=3; uncertain significance, n=3; pathogenic, n=8; other, n=1). Based on the evidence outlined above, the variant was classified as likely benign.
CeGaT Center for Human Genetics Tuebingen	RCV000079405	SCV001962680	pathogenic	not provided	2023-05-01	criteria provided, single submitter	clinical testing	G6PD: PM3:Very Strong, PM2:Supporting, PP1, PP4
Centogene AG - the Rare Disease Company	RCV000178823	SCV002028317	pathogenic	Anemia, nonspherocytic hemolytic, due to G6PD deficiency	2021-05-04	criteria provided, single submitter	clinical testing
Institute of Human Genetics, University of Leipzig Medical Center	RCV000178823	SCV002072537	likely pathogenic	Anemia, nonspherocytic hemolytic, due to G6PD deficiency	2022-01-12	criteria provided, single submitter	clinical testing	This variant was identified as hemizygous and together with NM_001042351.3:c.202G>A._x000D_ Criteria applied: PS4, PS3_MOD, PM5_SUP
AiLife Diagnostics, AiLife Diagnostics	RCV000079405	SCV002503162	uncertain significance	not provided	2021-07-02	criteria provided, single submitter	clinical testing
Dunham Lab, University of Washington	RCV000178823	SCV002599404	uncertain significance	Anemia, nonspherocytic hemolytic, due to G6PD deficiency	2022-08-12	criteria provided, single submitter	curation	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).
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	RCV000079405	SCV004026484	pathogenic	not provided	2022-06-23	criteria provided, single submitter	clinical testing
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	RCV000178823	SCV005044008	pathogenic	Anemia, nonspherocytic hemolytic, due to G6PD deficiency	2024-02-02	criteria provided, single submitter	clinical testing	PS3, PS4
OMIM	RCV000011073	SCV000031300	other	G6PD A+	2018-05-11	no assertion criteria provided	literature only
Division of Human Genetics, Children's Hospital of Philadelphia	RCV000178823	SCV000238427	pathogenic	Anemia, nonspherocytic hemolytic, due to G6PD deficiency	2015-02-20	no assertion criteria provided	research	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.
Division of Human Genetics, Children's Hospital of Philadelphia	RCV000477820	SCV000536703	pathogenic	Malaria, susceptibility to; Anemia, nonspherocytic hemolytic, due to G6PD deficiency	2015-12-29	no assertion criteria provided	research
Department Of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University	RCV000178823	SCV000891508	benign	Anemia, nonspherocytic hemolytic, due to G6PD deficiency	2017-12-30	no assertion criteria provided	curation
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City	RCV000178823	SCV001132890	pathogenic	Anemia, nonspherocytic hemolytic, due to G6PD deficiency	2019-08-25	no assertion criteria provided	clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV000079405	SCV001549316	uncertain significance	not provided		no assertion criteria provided	clinical testing	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.
GenomeConnect - Invitae Patient Insights Network	RCV000178823	SCV001749895	not provided	Anemia, nonspherocytic hemolytic, due to G6PD deficiency		no assertion provided	phenotyping only	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.
Zotz-Klimas Genetics Lab, MVZ Zotz Klimas	RCV000178823	SCV004099376	pathogenic	Anemia, nonspherocytic hemolytic, due to G6PD deficiency	2023-10-30	no assertion criteria provided	clinical testing