chrX-154533025-A-G

Position:

• chrX-154533025-A-G

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 9P and 1B. PP3 PP5_Very_Strong BP4

The NM_001360016.2(G6PD):​c.968T>C​(p.Leu323Pro) variant causes a missense change. The variant allele was found at a frequency of 0.000254 in 1,211,131 control chromosomes in the GnomAD database, including 1 homozygotes. There are 79 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.0015 (1 hom., 46 hem., cov: 25)
  • Exomes 𝑓: 0.00013 (0 hom. 33 hem.)
• Consequence: G6PD NM_001360016.2 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:15 U:1
• Conservation: PhyloP100: 3.80

Genes affected

G6PD (HGNC:4057): (glucose-6-phosphate dehydrogenase) This gene encodes glucose-6-phosphate dehydrogenase. This protein is a cytosolic enzyme encoded by a housekeeping X-linked gene whose main function is to produce NADPH, a key electron donor in the defense against oxidizing agents and in reductive biosynthetic reactions. G6PD is remarkable for its genetic diversity. Many variants of G6PD, mostly produced from missense mutations, have been described with wide ranging levels of enzyme activity and associated clinical symptoms. G6PD deficiency may cause neonatal jaundice, acute hemolysis, or severe chronic non-spherocytic hemolytic anemia. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_pathogenic. Variant got 8 ACMG points.

• PP3: Multiple lines of computational evidence support a deleterious effect 7: AlphaMissense, BayesDel_addAF, BayesDel_noAF, M_CAP, MutationAssessor, PROVEAN, REVEL [when max_spliceai, FATHMM_MKL, MetaRNN, MutationTaster was below the threshold]
• PP5: Variant X-154533025-A-G is Pathogenic according to our data. Variant chrX-154533025-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 10388.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154533025-A-G is described in Lovd as [Pathogenic].
• BP4: Computational evidence support a benign effect (MetaRNN=0.01999113). . Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
G6PD	NM_001360016.2	c.968T>C	p.Leu323Pro	missense_variant	9/13	ENST00000393562.10	NP_001346945.1
G6PD	NM_000402.4	c.1058T>C	p.Leu353Pro	missense_variant	9/13		NP_000393.4
G6PD	NM_001042351.3	c.968T>C	p.Leu323Pro	missense_variant	9/13		NP_001035810.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
G6PD	ENST00000393562.10	c.968T>C	p.Leu323Pro	missense_variant	9/13	1	NM_001360016.2	ENSP00000377192	P4

Frequencies

GnomAD3 genomes AF: 0.00150 AC: 170 AN: 112973 Hom.: 1 Cov.: 25 AF XY: 0.00131 AC XY: 46 AN XY: 35119

Gnomad AFR AF: 0.00456

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00212

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00329

GnomAD3 exomes AF: 0.000530 AC: 97 AN: 183074 Hom.: 1 AF XY: 0.000355 AC XY: 24 AN XY: 67648

Gnomad AFR exome AF: 0.00563

Gnomad AMR exome AF: 0.000766

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.000442

GnomAD4 exome AF: 0.000126 AC: 138 AN: 1098104 Hom.: 0 Cov.: 33 AF XY: 0.0000908 AC XY: 33 AN XY: 363514

Gnomad4 AFR exome AF: 0.00265

Gnomad4 AMR exome AF: 0.000966

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000119

Gnomad4 OTH exome AF: 0.000716

GnomAD4 genome AF: 0.00150 AC: 170 AN: 113027 Hom.: 1 Cov.: 25 AF XY: 0.00131 AC XY: 46 AN XY: 35183

Gnomad4 AFR AF: 0.00455

Gnomad4 AMR AF: 0.00212

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00325

Alfa AF: 0.000114 Hom.: 4

Bravo AF: 0.00175

ESP6500AA AF: 0.00548 AC: 21

ESP6500EA AF: 0.00 AC: 0

ExAC AF: 0.000593 AC: 72

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:15 Uncertain:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Anemia, nonspherocytic hemolytic, due to G6PD deficiency Pathogenic:5 Uncertain:1

Likely pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Nov 15, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Apr 08, 2021	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. -
Uncertain significance, flagged submission	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Aug 30, 2018	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Johns Hopkins Genomics, Johns Hopkins University	Sep 24, 2021	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. -
Pathogenic, criteria provided, single submitter	curation	Dunham Lab, University of Washington	Sep 01, 2024	Variant reported in hemizygote with G6PD deficiency, anemia, and jaundice (PP4). Heterozygous mother also reported to have decreased activity (PP1), and activity was decreased in red blood cells of hemizygote (51%) (PS3). Below expected carreier frequency in gnomAD (PM2). Predicted to be damaging by a consensus of tools (PP3). Reported as pathogenic by multiple clinical testing groups (PP5). Post_P 0.994 (odds of pathogenicity 1516.9, Prior_P 0.1). -

not provided Pathogenic:5

Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Apr 11, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Feb 10, 2014	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jul 01, 2024	G6PD: PM2, PS3:Moderate, PP1, PS4:Supporting -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Nov 30, 2022	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) -
Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Apr 19, 2022	- -

G6PD deficiency Pathogenic:3

Pathogenic, no assertion criteria provided	literature only	OMIM	Jun 01, 1988	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 11, 2019	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. -
Pathogenic, no assertion criteria provided	curation	Reproductive Health Research and Development, BGI Genomics	Jan 06, 2020	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; -

Malaria, susceptibility to Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Mar 18, 2024

- -

G6PD-related disorder Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Apr 09, 2024

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. This variant is interpreted as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.64
BayesDel_addAF	Pathogenic	0.31	D
BayesDel_noAF	Pathogenic	0.67
CADD	Uncertain	25
DANN	Uncertain	0.99
DEOGEN2	Pathogenic	0.98	D;D;D;.;D
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Benign	0.84	.;.;T;T;T
M_CAP	Pathogenic	0.91	D
MetaRNN	Benign	0.020	T;T;T;T;T
MetaSVM	Pathogenic	0.84	D
MutationAssessor	Pathogenic	3.1	M;M;M;.;.
MutationTaster	Benign	1.0	A;A;A;A
PrimateAI	Uncertain	0.62	T
PROVEAN	Pathogenic	-4.6	.;.;D;D;D
REVEL	Pathogenic	0.81
Sift	Benign	0.048	.;.;D;D;T
Sift4G	Benign	0.068	T;.;T;T;.
Polyphen		0.25	B;B;B;.;.
Vest4		0.88
MVP		1.0
MPC		1.7
ClinPred		0.11	T
GERP RS		5.6
Varity_R		0.97
gMVP		0.99

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs76723693; hg19: chrX-153761240;