rs137852339
Variant summary
Our verdict is Likely pathogenic. The variant received 9 ACMG points: 11P and 2B. PM1PP2PP5_Very_StrongBP4BS2_Supporting
The NM_001360016.2(G6PD):c.949G>A(p.Glu317Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000563 in 1,211,171 control chromosomes in the GnomAD database, including 7 homozygotes. There are 376 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_001360016.2 missense
Scores
Clinical Significance
Conservation
Publications
- anemia, nonspherocytic hemolytic, due to G6PD deficiencyInheritance: XL Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Ambry Genetics, Labcorp Genetics (formerly Invitae)
- G6PD deficiencyInheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
- class I glucose-6-phosphate dehydrogenase deficiencyInheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Likely_pathogenic. The variant received 9 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001360016.2. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| G6PD | NM_001360016.2 | MANE Select | c.949G>A | p.Glu317Lys | missense | Exon 9 of 13 | NP_001346945.1 | ||
| G6PD | NM_000402.4 | c.1039G>A | p.Glu347Lys | missense | Exon 9 of 13 | NP_000393.4 | |||
| G6PD | NM_001042351.3 | c.949G>A | p.Glu317Lys | missense | Exon 9 of 13 | NP_001035810.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| G6PD | ENST00000393562.10 | TSL:1 MANE Select | c.949G>A | p.Glu317Lys | missense | Exon 9 of 13 | ENSP00000377192.3 | ||
| G6PD | ENST00000696421.1 | c.949G>A | p.Glu317Lys | missense | Exon 9 of 13 | ENSP00000512616.1 | |||
| G6PD | ENST00000369620.6 | TSL:5 | c.1087G>A | p.Glu363Lys | missense | Exon 9 of 13 | ENSP00000358633.2 |
Frequencies
GnomAD3 genomes AF: 0.000257 AC: 29AN: 113000Hom.: 0 Cov.: 24 show subpopulations
GnomAD2 exomes AF: 0.00124 AC: 227AN: 183230 AF XY: 0.00195 show subpopulations
GnomAD4 exome AF: 0.000595 AC: 653AN: 1098117Hom.: 7 Cov.: 33 AF XY: 0.000979 AC XY: 356AN XY: 363511 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.000257 AC: 29AN: 113054Hom.: 0 Cov.: 24 AF XY: 0.000568 AC XY: 20AN XY: 35206 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Anemia, nonspherocytic hemolytic, due to G6PD deficiency Pathogenic:12
Variant found in unrelated hemizygotes with G6PD deficiency but no other symptoms (PS4_M, PP4). Also segregates with deficiency in multiple brothers, and heterozygous sister has slightly decreased activity (PP1). Decreased activity in red blood cells of hemizygotes (19-52%) (PS3). Modeling predicts disruption of function (PP3). Reported as pathogenic by multiple clinical testing groups (PP5). Post_P 0.994 (odds of pathogenicity 1517, Prior_P 0.1).
The observed missense variant c.949G>A (p.Glu317Lys) in G6PD gene has been reported previously in multiple individuals affected with Glucose-6-phosphate dehydrogenase (G6PD) deficiency (Sarker SK, et al., 2016, Islam MT, et al., 2018). This variant is a prevalent G6PD variant in the South Asian population, typically associated with partial reduction of enzyme activity (Sarker SK, et al., 2016, Islam MT, et al., 2018). The p.Glu317Lys variant is present with allele frequency of 0.1% in gnomAD Exomes. This variant has been submitted to the ClinVar database as Pathogenic (multiple submissions). The reference amino acid change at this position on G6PD gene is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Glutamic acid at position 317 is changed to a Lysine changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Pathogenic.
This variant in exon 9 of the G6PD gene results in the amino acid substitution from glutamic acid to lysine at codon 347 (p.Glu347Lys) with the sequence change of c.1039G>A (NM_000402.4). This variant was observed in a proband with a decreased level of G6PD enzyme (3.1 U/dl) which was screened for advanced newborn screening with confirmatory genetic reflex testing at Lifecell diagnostics. There is a small physicochemical difference between glutamic acid and lysine. The observed variant is not present in both the 1000 Genomes and gnomAD databases. The reference base is conserved across the species and in-silico predictions by Polyphen and SIFT are damaging. This is a Class III variant associated with moderate G6PD deficiency (10-60% enzyme activity) and hemolysis with stressors only. According to the previous studies this variant is also known as G6PD Kerala, G6PD Kalyan, G6PD Kerala Kalyan, G6PD Jamnaga, and G6PD Rohini. This variant has previously been reported for Glucose-6- phosphate dehydrogenase (G6PD) deficiency by Islam MT et al., 2018. The Missense Variants Z-Score for this variant is 2.60. Missense Variants Z-Score is produced by the Exome Aggregation Consortium (60,706 adult humans) by computing a signed Z score for the deviation of observed counts from the expected number. Positive Z scores indicate increased constraint (intolerance to variation) and therefore that the gene had fewer missense variants than expected. This variant is a prevalent G6PD variant in the South Asian population, typically associated with partial reduction of enzyme activity (Ahluwalia A et al. 1992; PMID: 1303182), (Islam MT et al. 2018; PMID: 30097005), ( Ninokata A et al, 2006; PMID: 16528451), ( Sukumar S et al. 2004; PMID: 15315792), ( Sarker SK et al. 2016; PMID: 27880809), (Minucci A et al, 2012; PMID: 22293322).
This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 317 of the G6PD protein (p.Glu317Lys). This variant is present in population databases (rs137852339, gnomAD 1.1%), and has an allele count higher than expected for a pathogenic variant. This variant is a prevalent G6PD variant in the South Asian population, typically associated with partial reduction of enzyme activity (PMID: 1303182, 30097005, 16528451, 15315792, 30097005, 27880809, 27535533). By WHO classification, this is a Class III variant associated with moderate G6PD deficiency (10-60% enzyme activity) and hemolysis with stressors only (PMID: 22293322). This variant is also known as G6PD Kerala, G6PD Kalyan, G6PD Kerala–Kalyan, G6PD Jamnaga, and G6PD Rohini. ClinVar contains an entry for this variant (Variation ID: 10401). Invitae Evidence 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 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. For these reasons, this variant has been classified as Pathogenic.
The hemizygous, maternally inherited c.949G>A p.(Glu317Lys) variant identified in the G6PD gene substitutes an evolutionarily conserved glutamic acid with Lysine at position 317/516 (exon 9/13) in the dimer interface region [PMID: 31294066] of the encoded protein. This variant is also called c.1039G>Ap.(Glu347Lys) based on transcript NM_000402.4, and is reported in ClinVar [ClinVar ID:10401] as Pathogenic. This variant is observed in 322 alleles (0.04% minor allele frequency with 6 homozygotes and 151 hemizygotes) in population databases (gnomAD v2.1.1 and v3.1.2, TOPMed Freeze 8, All of Us) including in 242 alleles(1.07% minor allele frequency with 1 homozygote and 148 hemizygotes) in South Asian subpopulation (gnomAD v2.1.1 and v3.1.2(non-Topmed)). In silico predictions are in favor of damaging effect for p.(Glu317Lys) (REVEL = 0.648). The p.(Glu317Lys) variant in G6PD has previously been reported in individuals with G6PD deficiency and is also known as G6PD Kerala, G6PD Kalyan, G6PD Kerala Kalyan, G6PD Jamnagar, and G6PD Rohini in the literature [(PMID: 15996881, 1303182, 30097005,16528451, 15315792, 27880809, 27535533, 33069889]. The c.949G>A p.(Glu317Lys) variant in G6PD is reported as Class III variant according to WHO classification and associated with moderate G6PD deficiency (10-60% enzyme activity) and hemolysis with stressors only [PMID:15996881,22293322]. Based on available evidence this maternally inherited hemizygous c.949G>A p.(Glu317Lys) variant identified in the G6PD gene is classified as Pathogenic.
This variant is classified as Pathogenic. Evidence in support of pathogenic classification: This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has previously been classified as a G6PD Class III variant and is known as the Kerala-Kalyan variant. Individuals with this variant have moderate to mild G6PD enzyme activity (WHO recommendations; G6PD database; PMID: 22293322; 30097005, 31833391). Additional information: Variant is predicted to result in a missense amino acid change from Glu to Lys; This variant is heterozygous; This gene is associated with X-linked recessive disease; Variant is present in gnomAD >=0.01 and <0.03 for a recessive condition (v4: 292 heterozygote(s), 7 homozygote(s), 376 hemizygote(s)); Variant is located in the annotated G6PD C-terminal domain (DECIPHER); Missense variant with conflicting in silico predictions and uninformative conservation; Loss of function is a known mechanism of disease in this gene and is associated with G6PD deficient congenital nonspherocytic haemolytic anaemia 1 (MIM#300908); This variant has been shown to be maternally inherited by trio analysis.
not provided Pathogenic:4
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Class III variant according to the WHO classification system, associated with moderate G6PD deficiency (10-60% enzyme activity) and hemolysis with stressors only (PMID: 22293322); Previously described as G6PD Kerala, G6PD Kalyan, G6PD Kerala-Kalyan, G6PD Jamnagar, and G6PD Rohini (PMID: 1303182, 15996881); This variant is associated with the following publications: (PMID: 32036089, 30097005, 36508454, 34551338, 34620237, 33069889, 20713184, 27880809, 27535533, 17233850, 1303182, 15996881, 22293322, 36681081, 38312194, 38488835)
G6PD: PP1:Strong, PS4, PS3:Moderate
G6PD deficiency Pathogenic:2
The G6PD c.1039G>A (p. Glu347Lys) missense variant, which is also commonly reported as c.949G>A (p.Glu317Lys) and G6PD Kerala-Kalyan, and less commonly reported as G6PD Jamnagar or Rohini, is one of the most common disease-causing variants in South Asian populations. The p.Glu347Lys variant has been estimated to account for between 1.1% and 24.5% of disease-causing alleles in the Indian population (Sukumar et al. 2004; Devendra et al. 2020). This variant has also been reported in affected individuals of Bangladeshi, Burmese, and Thai descent (Nuchprayoon et al. 2008; Sarker et al. 2016). The p.Glu347Lys variant is typically associated with glucose-6-phosphate dehydrogenase enzyme activity levels between 10% - 60% of wild type and is considered a class III variant according the WHO classification system for G6PD variants (Minucci et al. 2012; Harcke et al. 2019). The p.Glu347Lys variant is reported at a frequency of 0.01138 in the South Asian population of the Genome Aggregation Database. This allele frequency is high but is consistent with the disease prevalence estimates. Although the consequences of p.Glu347Lys have not been characterized experimentally, the Glu347 residue is known to interact with Lys275, which is the site of the another disease-causing variant, p.Lys275Asn or G6PD Bangkok. This interaction forms a salt bridge between subunits B and C of the tetrameric structure in wild-type G6PD (Boonyuen et al. 2017). Based on the collective evidence and application of the ACMG criteria, the p. Glu347Lys variant is classified as pathogenic for glucose-6-phosphate dehydrogenase deficiency.
Variant summary: G6PD c.1039G>A (p.Glu347Lys) results in a conservative amino acid change in the encoded protein sequence. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change. The variant allele was found at a frequency of 0.0012 in 183230 control chromosomes in the gnomAD database, including 1 homozygotes. This frequency is not significantly higher than estimated for a pathogenic variant in G6PD causing Glucose 6 Phosphate Dehydrogenase Deficiency (0.0012 vs 0.29), allowing no conclusion about variant significance. c.1039G>A (also known as G6PD Kerala-Kalyan) has been observed in multiple individuals affected with Glucose 6 Phosphate Dehydrogenase Deficiency (example: Sukumar_2004). These data indicate that the variant is very likely to be associated with disease. The following publication has been ascertained in the context of this evaluation (PMID: 15315792). ClinVar contains an entry for this variant (Variation ID: 10401). Based on the evidence outlined above, the variant was classified as pathogenic.
Malaria, susceptibility to;C2720289:Anemia, nonspherocytic hemolytic, due to G6PD deficiency Pathogenic:1
Malaria, susceptibility to Pathogenic:1
Congenital nonspherocytic hemolytic anemia Pathogenic:1
No clinically relevant variants in concordance with the observed phenotype were found in proband. However, a known missense variant, c.949G>A p.(Glu317Lys) in exon 9 of G6PD (NM_001360016.2) was observed in hemizygous state in the proband (Arunachalam et al., 2019; Minucci et al., 2012). Sanger validation and segregation analysis showed that the variant is found in hemizygous state in the proband, heterozygous state in his mother (Lab ID-10044) and absent in his father (Lab ID-10045). This variant is present in 682 individuals in heterozygous state, 376 individuals in hemizygous state, and 7 individuals in homozygous state in gnomAD (v4.1.0). Also, the variant is present in 41 individuals in heterozygous state and 23 individuals in hemizygous/homozygous state in our in-house database of 3464 exomes. Individuals with disease-causing variants in G6PD may be asymptomatic, however may develop severe hemolysis when exposed to oxidative agents which include certain foods and medications.
G6PD KERALA Other:1
G6PD KERALA-KALYAN Other:1
G6PD KALYAN Other:1
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at