rs76645461
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM1PP3_ModeratePP5_Very_Strong
The NM_001360016.2(G6PD):c.143T>C(p.Ile48Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000141 in 1,209,926 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Genomes: 𝑓 0.0000089 ( 0 hom., 0 hem., cov: 23)
Exomes 𝑓: 0.000015 ( 0 hom. 5 hem. )
Consequence
G6PD
NM_001360016.2 missense
NM_001360016.2 missense
Scores
7
2
4
Clinical Significance
Conservation
PhyloP100: 7.09
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]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PM1
?
In a hotspot region, there are 4 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 1 uncertain in NM_001360016.2
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.925
PP5
?
Variant X-154536156-A-G is Pathogenic according to our data. Variant chrX-154536156-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 10402.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-154536156-A-G is described in Lovd as [Pathogenic]. Variant chrX-154536156-A-G is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
G6PD | NM_001360016.2 | c.143T>C | p.Ile48Thr | missense_variant | 3/13 | ENST00000393562.10 | |
G6PD | NM_000402.4 | c.233T>C | p.Ile78Thr | missense_variant | 3/13 | ||
G6PD | NM_001042351.3 | c.143T>C | p.Ile48Thr | missense_variant | 3/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
G6PD | ENST00000393562.10 | c.143T>C | p.Ile48Thr | missense_variant | 3/13 | 1 | NM_001360016.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000895 AC: 1AN: 111765Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33947
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GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183351Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67819
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GnomAD4 exome AF: 0.0000146 AC: 16AN: 1098104Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 5AN XY: 363460
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ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:13Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Anemia, nonspherocytic hemolytic, due to G6PD deficiency Pathogenic:7
Pathogenic, no assertion criteria provided | clinical testing | Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City | Jan 29, 2019 | - - |
Pathogenic, criteria provided, single submitter | curation | Dunham Lab, University of Washington | Aug 12, 2022 | Variant found in unrelated hemizygotes with deficiency, some with anemia and jaundice (PP4, PS4_M). Decreased activity in red blood cells (3-35%) (PS3). In silico analysis supports that this missense variant has a deleterious effect (PP3). Below expected carrier frequency in gnomAD (PM2). Reported as pathogenic by multiple clinical testing groups (PP5). Post_P 0.997 (odds of pathogenicity 3155, Prior_P 0.1). - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | May 17, 2023 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Mendelics | May 27, 2022 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Dec 29, 2023 | This sequence change replaces isoleucine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 48 of the G6PD protein (p.Ile48Thr). This variant is present in population databases (rs76645461, gnomAD 0.02%). This missense change has been observed in individuals with glucose-6-phosphate dehydrogenase (G6PD) deficiency (PMID: 8490627, 16119988, 22018328, 22963789). This variant is also known as the Aures variant. ClinVar contains an entry for this variant (Variation ID: 10402). Advanced 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 at Invitae 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. Experimental studies have shown that this missense change affects G6PD function (PMID: 8490627, 22963789). For these reasons, this variant has been classified as Pathogenic. - |
Pathogenic, criteria provided, single submitter | research | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | Mar 17, 2024 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Jul 27, 2020 | This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. - |
not provided Pathogenic:3
Pathogenic, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jan 23, 2015 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Apr 08, 2023 | 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: 20236109, 8787363, 27853304, 12972027, 8860007, 16119988, 22963789, 22018328, 23006493, 21931771, 27884173, 8490627, 34272389, 31589614, 28902532) - |
Pathogenic, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Dec 01, 2021 | The G6PD c.143T>C; p.Ile48Thr variant (rs76645461), also known as G6PD Aures, is reported in the literature in multiple individuals affected with G6PD deficiency (Alfadhli 2005, Al-Jaouni 2011, Benmansour 2013, Nafa 1993). Individuals with this variant have reduced G6PD enzyme activity and is classified as a WHO Class III variant (Benmansour 2013). This variant is also reported in ClinVar (Variation ID: 10402) and is found in the East Asian population with an allele frequency of 0.01% (2/13861 alleles) in the Genome Aggregation Database. The isoleucine at codon 48 is highly conserved, and computational analyses predict that this variant is deleterious (REVEL: 0.8). Based on available information, this variant is considered to be pathogenic. References: Alfadhli S et al. Molecular characterization of glucose-6-phosphate dehydrogenase gene defect in the Kuwaiti population. Arch Pathol Lab Med. 2005 Sep;129(9):1144-7. PMID: 16119988. Al-Jaouni SK et al. Molecular characterization of glucose-6-phosphate dehydrogenase deficiency in Jeddah, Kingdom of Saudi Arabia. BMC Res Notes. 2011 Oct 24;4:436. PMID: 22018328. Benmansour I et al. Two new class III G6PD variants [G6PD Tunis (c.920A>C: p.307Gln>Pro) and G6PD Nefza (c.968T>C: p.323 Leu>Pro)] and overview of the spectrum of mutations in Tunisia. Blood Cells Mol Dis. 2013 Feb;50(2):110-4. PMID: 22963789. Nafa K et al. G6PD Aures: a new mutation (48 Ile-->Thr) causing mild G6PD deficiency is associated with favism. Hum Mol Genet. 1993 Jan;2(1):81-2. PMID: 8490627. - |
Malaria, susceptibility to;C2720289:Anemia, nonspherocytic hemolytic, due to G6PD deficiency Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Nov 11, 2021 | - - |
Malaria, susceptibility to Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Oct 26, 2023 | - - |
G6PD deficiency Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 16, 2021 | The G6PD c.233T>C (p.Ile78Thr) variant is a missense variant. Across a selection of the available literature, this variant, which is also known as the G6PD Aures variant, has been reported in 92 individuals with glucose-6-phosphate dehydrogenase deficiency, including in a hemizygous state in 66 males, in a homozygous state in 15 females, and in 11 cases of unspecified sex/zygosity (Nafa et al. 1993; AlFadhli et al. 2005; Al-Jaouni et al. 2011; Dallol et al. 2012; Benmansour et al. 2013; Sanephonasa et al. 2021). The p.Ile78Thr variant is reported at a frequency of 0.000144 in the East Asian population of the Genome Aggregation Database (version 2.1.1), but this frequency is based on only two alleles in a region of good sequencing coverage. Multiple in silico algorithms consistently predict a functional consequence of this variant, and carriers of this variant have been confirmed to have reduced G6PD enzyme activity (Dallol et al. 2012). Based on the available evidence, the p.Ile78Thr variant is classified as pathogenic for glucose-6-phosphate dehydrogenase deficiency. - |
G6PD AURES Other:1
other, no assertion criteria provided | literature only | OMIM | Apr 18, 2013 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Uncertain
Dann
Benign
DEOGEN2
Pathogenic
D;D;D;.;D;.;D
FATHMM_MKL
Uncertain
D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D;D;D;D;D
MetaSVM
Pathogenic
D
MutationAssessor
Benign
L;L;L;L;.;.;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Pathogenic
D
Sift4G
Benign
T;.;T;T;.;.;.
Polyphen
D;D;D;.;.;.;.
Vest4
MutPred
Gain of disorder (P = 0.0198);Gain of disorder (P = 0.0198);Gain of disorder (P = 0.0198);Gain of disorder (P = 0.0198);Gain of disorder (P = 0.0198);Gain of disorder (P = 0.0198);Gain of disorder (P = 0.0198);
MVP
MPC
0.80
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
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Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at