Submissions for variant NM_001360016.2(G6PD):c.968T>C (p.Leu323Pro)

gnomAD frequency: 0.00154  dbSNP: rs76723693

Total submissions: 14

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Eurofins Ntd Llc (ga)	RCV000757319	SCV000233011	pathogenic	not provided	2014-02-10	criteria provided, single submitter	clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000757319	SCV000885492	pathogenic	not provided	2022-04-11	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000011119	SCV000915298	likely pathogenic	G6PD deficiency	2019-01-11	criteria provided, single submitter	clinical testing	The G6PD c.968T>C (p.Leu323Pro) variant is a missense variant. Benmansour et al. (2013) reported the variant in a heterozygous state in two individuals with glucose-6-phosphate dehydrogenase (G6PD) deficiency as well as in a hemizygous state in one individual with a measured residual enzyme activity of 51% of wildtype. The p.Leu323Pro variant is commonly referred to as G6PD Nefza. This variant is more commonly reported in cis with another variant, p.Asn126Asp, which is referred to as G6PD A-; this complex allele has been identified in 76/1039 (7%) of individuals with G6PD deficiency (Beutler et al. 1989; Hamel et al. 2002; Monteiro et al. 2014; Reading et al. 2017). The p.Leu323Pro variant is reported at a frequency of 0.009970 in the African population of the 1000 Genomes Project. Functional studies in E. coli demonstrated the p.Leu323Pro variant shows 50% residual activity compared to the wildtype enzyme and results in reduced substrate affinity and G6PD expression (Ramirez-Nava et al. 2017). Importantly, comprehensive studies of the p.Leu323Pro, p.Asn126Asp, and complex alleles suggested the p.Leu323Pro variant was the primary contributor to the alterations in catalytic activity and structural modifications observed for the complex allele. Based on the available evidence, the p.Leu323Pro variant is classified as likely pathogenic for glucose-6-phosphate dehydrogenase deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Invitae	RCV000818410	SCV000959021	uncertain significance	Anemia, nonspherocytic hemolytic, due to G6PD deficiency	2018-08-30	criteria provided, single submitter	clinical testing	This sequence change replaces leucine with proline at codon 323 of the G6PD protein (p.Leu323Pro). The leucine residue is moderately conserved and there is a moderate physicochemical difference between leucine and proline. This variant is present in population databases (rs76723693, ExAC 0.6%). The c.968T>C (p.Leu323Pro) variant and the c.376A>G (p.Asn126Asp) variant, when co-occurring in cis, is known as G6PD Betica or G6PD Selma c.[376A>G; 968T>C], which is a subtype of the G6PD A- haplotype (PMID: 18056001, 2572288, 25915902, 27413522). The c.[376A>G; 968T>C] G6PD A- haplotype is the most prevalent G6PD deficiency variant in the Gambian population at 7% (PMID: 24615128, 26738565, 28067620). This variant alone has been reported in an individual affected with neonatal jaundice and hemolytic anemia triggered by fava beans (favism) (PMID: 22963789). ClinVar contains an entry for this variant (Variation ID: 10388). While the c.968T>C (p.Leu323Pro) variant alone has been shown to only mildly affect enzyme activity, the c.[376A>G; 968T>C] changes of the G6PD A- haplotype have been reported to act synergistically to cause dramatic reduction of the enzymatic activity of the G6PD protein (PMID: 18177777, 2633878, 2572288, 28067620, 28195434). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Mendelics	RCV000818410	SCV001142105	pathogenic	Anemia, nonspherocytic hemolytic, due to G6PD deficiency	2019-05-28	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000818410	SCV001572468	pathogenic	Anemia, nonspherocytic hemolytic, due to G6PD deficiency	2021-04-08	criteria provided, single submitter	clinical testing	Variant summary: G6PD c.1058T>C (p.Leu353Pro) results in a non-conservative amino acid change located in the C-terminal domain (IPR022675) of the encoded protein sequence. This variant has also been reported in the literature as c.968T>C (p.Leu323Pro) in transcript NM_001042351, and has been referred to as G6PD-Nefza. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00053 in 183074 control chromosomes in the gnomAD database, including 1 homozygote. c.1058T>C has been reported in the literature in multiple individuals affected with G6PD Deficiency. In most of these individuals, the variant was found in cis with a second variant in G6PD, c.466A>G (p.Asn156Asp; also known as c.376A>G, p.Asn126Asp) (e.g. Beutler_1989, Xu_1995, Vulliamy_1996, Rodrigues_2002, DeAraujo_2006, Jalloh_2008, Benkerrou_2013, Dijgo_2019). This complex allele [c.466A>G, c.1058T>C] has been referred to as "G6PD Betica or "G6PD Betica-Selma" in the literature. Experimental evidence has reported a reduction in G6PD activity in cells expressing either [c.466A>G, c.1058T>C] or c.1058T>C in isolation. In the same study, c.1058T>C was also shown to significantly reduce affinity for substrates G6P and NADP+ (Ramirez-Nava_2017). At least one publication reports the c.1058T>C variant in isolation in an individual who was diagnosed with hemolytic anemia after ingestion of fava beans (Benmansour_2013). This patient had a family history of G6PD deficiency, and G6PD activity in his cells was assessed to be approximately 51% that of wild-type. Collectively, these findings indicate that c.1058T>C is very likely to be associated with disease. Six other clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, citing the variant as pathogenic/likely pathogenic (n=5) and uncertain significance (n=1). Based on the evidence outlined above, the variant was classified as pathogenic.
GeneDx	RCV000757319	SCV001873905	likely pathogenic	not provided	2022-11-30	criteria provided, single submitter	clinical testing	Typically seen in cis with the N126D variant, which has also been reported in cis with other G6PD variants in individuals with G6PD deficiency, and does not lead to symptoms when present without a second variant (Mason et al., 2007); Functional studies demonstrate that L323P is associated with decreased G6PD activity and a lower catalytic constant, which is greater than that seen with N126D by itself, but is even more pronounced when the two variants are found in combination (Ramirez-Nava et al., 2017); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 26738565, 19782058, 22237549, 35685917, 34451395, 32387609, 32702756, 24615128, 22963789, 21931771, 22009270, 11852882, 27941691, 27267757, 2572288, 28195434, 23006493, 17611006, 25071003, 21929367, 29072585, 25141282, 22963798, 18177777, 12367584, 2633878, 3393536, 2836867, 30206300, 31525211, 30204801, 30409136, 30508000, 30071859, 28067620, 31564435, 33072997, 30755392, 31589614, 31539204, 28902532, 33887194, 33637102, 35313643, 34844289, 35199448)
Revvity Omics, Revvity	RCV000818410	SCV002025186	likely pathogenic	Anemia, nonspherocytic hemolytic, due to G6PD deficiency	2023-11-15	criteria provided, single submitter	clinical testing
Johns Hopkins Genomics, Johns Hopkins University	RCV000818410	SCV002051813	likely pathogenic	Anemia, nonspherocytic hemolytic, due to G6PD deficiency	2021-09-24	criteria provided, single submitter	clinical testing	c.[376A>G;968T>C] is a complex allele containing two G6PD variants (rs76723693; rs1050829) that are located on the same chromosome (in cis). Each variant has an entry in ClinVar. c.968T>C is rare (<0.1%) in a large population dataset (gnomAD: 127/205036 total alleles, 0.06%, 1 homozygote, 32 hemizygotes), while c.376A>G is polymorphic (3.2%) in most ancestral populations. This complex allele, sometimes referred to as "G6PD Betica-Selma", has been identified in approximately 7% of individuals with G6PD deficiency. In vitro functional studies have shown a reduction in G6PD activity (less than 50% enzyme activity) in cells expressing either c.[376A>G;968T>C] or c.968T>C in isolation. At least one publication reports the c.968T>C variant in isolation in an individual who was affected with neonatal jaundice and hemolytic anemia after ingestion of fava beans. This person had a family history of G6PD deficiency, and G6PD activity in his cells was approximately 51% that of wild type, consistent with a Class III variant (10-60% enzyme activity). c.376A>G has not been identified in isolation in affected individuals, but may act synergistically with other G6PD variants. Based on the available evidence, we consider this complex allele, which combines c.376A>G and c.968T>C, to be likely pathogenic.
Dunham Lab, University of Washington	RCV000818410	SCV002599252	likely pathogenic	Anemia, nonspherocytic hemolytic, due to G6PD deficiency	2022-08-12	criteria provided, single submitter	curation	Variant found in hemizygote with G6PD deficiency, anemia, and jaundice (PP4). Heterozygous mother has decreased activity (PP1), and activity is decreased in red blood cells of hemizygote (51%) (PS3). Below expected carreier frequency in gnomAD (PM2). Reported as pathogenic by multiple clinical testing groups (PP5). Post_P 0.988 (odds of pathogenicity 728.3, Prior_P 0.1).
Baylor Genetics	RCV003460453	SCV004195387	pathogenic	Malaria, susceptibility to	2023-10-25	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV003934822	SCV004751952	pathogenic	G6PD-related condition	2023-11-19	criteria provided, single submitter	clinical testing	The G6PD c.968T>C variant is predicted to result in the amino acid substitution p.Leu323Pro. The c.968T>C variant, when present on the same allele as the c.376A>G variant is together also referred to as G6PD Betica and is causative for glucose-6-phosphate dehydrogenase deficiency (Manco et al. 2007. PubMed ID: 18056001; Moradkhani et al. 2012. PubMed ID: 22139979). This variant is reported in 0.54% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/X-153761240-A-G). This variant is interpreted as pathogenic.
OMIM	RCV000011119	SCV000031346	pathogenic	G6PD deficiency	1988-06-01	no assertion criteria provided	literature only
Reproductive Health Research and Development, BGI Genomics	RCV000011119	SCV001142505	pathogenic	G6PD deficiency	2020-01-06	no assertion criteria provided	curation	NM_001042351.1:c.968T>C in the G6PD gene has an allele frequency of 0.005 in African subpopulation in the gnomAD database. This variant is more commonly reported in cis with another variant, p.Asn126Asp, which is referred to as G6PD A-; this complex allele has been identified in 76/1039 (7%) of individuals with G6PD deficiency (PMID: 2572288; 12367584; 25141282; 28195434). Functional studies demonstrated the p.Leu323Pro has a major contribution to the loss of affinity for both substrates in the double mutant G6PD A- (PMID29072585). Pathogenic computational verdict because 9 pathogenic predictions from DANN, DEOGEN2, FATHMM-MKL, M-CAP, MVP, MutationAssessor, MutationTaster, REVEL and SIFT. Taken together, we interprete this variant as Pathogenic/Likely pathogenic. ACMG/AMP Criteria applied: PS3; PS4; PP4; PP3;