ClinVar Genomic variation as it relates to human health
NM_000402.4(G6PD):c.1478G>A (p.Arg493His)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000402.4(G6PD):c.1478G>A (p.Arg493His)
Variation ID: 100059 Accession: VCV000100059.52
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: Xq28 X: 154532257 (GRCh38) [ NCBI UCSC ] X: 153760472 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Jun 28, 2015 May 12, 2024 Jan 19, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001360016.2:c.1388G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001346945.1:p.Arg463His missense NM_000402.4:c.1478G>A NP_000393.4:p.Arg493His missense NM_001042351.3:c.1388G>A NP_001035810.1:p.Arg463His missense NM_001360016.1:c.1388G>A NC_000023.11:g.154532257C>T NC_000023.10:g.153760472C>T NG_009015.2:g.20316G>A - Protein change
- R463H, R493H
- Other names
- G6PD, ARG463HIS
- G6PD Anant
- G6PD Dhon
- G6PD Kaiping
- G6PD Petrich-like
- G6PD Sapporo-like
- G6PD Wosera
- Canonical SPDI
- NC_000023.11:154532256:C:T
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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0.00132 (T)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
The Genome Aggregation Database (gnomAD) 0.00012
Trans-Omics for Precision Medicine (TOPMed) 0.00013
Exome Aggregation Consortium (ExAC) 0.00045
The Genome Aggregation Database (gnomAD), exomes 0.00055
1000 Genomes Project 30x 0.00125
1000 Genomes Project 0.00132
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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G6PD | - | - |
GRCh38 GRCh37 |
636 | 948 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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G6PD ANANT
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other (1) |
no assertion criteria provided
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May 24, 2017 | RCV000011121.12 |
G6PD PETRICH-LIKE
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other (1) |
no assertion criteria provided
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May 24, 2017 | RCV000011123.12 |
G6PD SAPPORO-LIKE
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other (1) |
no assertion criteria provided
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May 24, 2017 | RCV000011124.12 |
G6PD KAIPING
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other (1) |
no assertion criteria provided
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May 24, 2017 | RCV000011120.12 |
G6PD DHON
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other (1) |
no assertion criteria provided
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May 24, 2017 | RCV000011122.12 |
Pathogenic (4) |
criteria provided, multiple submitters, no conflicts
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Sep 5, 2023 | RCV000174271.30 | |
Pathogenic (6) |
criteria provided, multiple submitters, no conflicts
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Jan 19, 2024 | RCV000823393.26 | |
Pathogenic (1) |
criteria provided, single submitter
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Oct 31, 2018 | RCV000763201.10 | |
Pathogenic (2) |
criteria provided, single submitter
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Apr 25, 2023 | RCV000991190.10 | |
Pathogenic (1) |
criteria provided, single submitter
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Jun 10, 2016 | RCV001266661.10 | |
Pathogenic (1) |
criteria provided, single submitter
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Oct 26, 2023 | RCV003460789.1 | |
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Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Oct 31, 2018)
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criteria provided, single submitter
Method: clinical testing
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Anemia, nonspherocytic hemolytic, due to G6PD deficiency
Malaria, susceptibility to
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV000893820.1
First in ClinVar: Mar 31, 2019 Last updated: Mar 31, 2019 |
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Pathogenic
(May 16, 2013)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Eurofins Ntd Llc (ga)
Accession: SCV000225547.5
First in ClinVar: Jun 28, 2015 Last updated: Jun 28, 2015 |
Number of individuals with the variant: 6
Sex: mixed
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Pathogenic
(May 04, 2022)
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criteria provided, single submitter
Method: clinical testing
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Anemia, nonspherocytic hemolytic, due to G6PD deficiency
Affected status: unknown
Allele origin:
germline
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Mendelics
Accession: SCV002516408.1
First in ClinVar: May 28, 2022 Last updated: May 28, 2022 |
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Pathogenic
(Feb 02, 2022)
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criteria provided, single submitter
Method: clinical testing
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Anemia, nonspherocytic hemolytic, due to G6PD deficiency
(X-linked recessive inheritance)
Affected status: no
Allele origin:
germline
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Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV002557889.1
First in ClinVar: Aug 08, 2022 Last updated: Aug 08, 2022 |
Comment:
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism … (more)
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with G6PD deficient haemolytic anaemia (favism) (MIM#300908). (I) 0109 - This gene is associated with X-linked recessive disease. Hemizygous males and homozygous females are commonly affected, however some heterozygous female carriers can also be affected depending on X inactivation. (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to histidine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (v2: 71 heterozygotes, 1 homozygote, 33 hemizygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2: 0 heterozygotes, 0 homozygotes, 1 hemizygote). (I) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated glucose-6-phosphate dehydrogenase, C-terminal domain (DECIPHER). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. Also known as the Kaiping variant, it is one the most common pathogenic alleles amongst the Chinese population; and is classified as a WHO class II variant (severe deficiency). In addition, it is consistently classified as pathogenic by diagnostic laboratories in ClinVar (PMID: 33051526). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign (less)
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Pathogenic
(Aug 12, 2022)
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criteria provided, single submitter
Method: curation
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Anemia, nonspherocytic hemolytic, due to G6PD deficiency
Affected status: yes
Allele origin:
inherited
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Dunham Lab, University of Washington
Accession: SCV002599397.1
First in ClinVar: Nov 13, 2022 Last updated: Nov 13, 2022 |
Comment:
Variant found in unrelated hemizygotes with deficiency, some with anemia, jaundice, and favism, and one with CNSHA (PS4_M, PP4). Segregates with deficiency in a family … (more)
Variant found in unrelated hemizygotes with deficiency, some with anemia, jaundice, and favism, and one with CNSHA (PS4_M, PP4). Segregates with deficiency in a family (PP1). Decreased activity in red blood cells (1-44%) and when expressed in E. coli (PS3). Predicted to be disease causing by Mutation Taster and probably damaging by PolyPhen (PP3). Below expected carrier frequency in gnomAD (PM2). Reported as pathogenic by multiple clinical testing groups (PP5). Post_P 0.999 (odds of pathogenicity 6563, Prior_P 0.1). (less)
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Pathogenic
(Jun 10, 2016)
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criteria provided, single submitter
Method: clinical testing
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Inborn genetic diseases
Affected status: yes
Allele origin:
germline
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Ambry Genetics
Accession: SCV001444838.2
First in ClinVar: Nov 21, 2020 Last updated: Jan 07, 2023 |
Number of individuals with the variant: 1
Clinical Features:
Muscular hypotonia (present) , Dysarthria (present) , Hyperbilirubinemia (present) , Dystonia (present) , Spasticity (present) , Athetoid cerebral palsy (present) , Failure to thrive (present) … (more)
Muscular hypotonia (present) , Dysarthria (present) , Hyperbilirubinemia (present) , Dystonia (present) , Spasticity (present) , Athetoid cerebral palsy (present) , Failure to thrive (present) , Gastroesophageal reflux (present) , Dyskinesia (present) , Difficulty walking (present) , Movement disorder (present) (less)
Sex: male
Ethnicity/Population group: Asian
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Pathogenic
(Sep 05, 2023)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV001982609.3
First in ClinVar: Oct 30, 2021 Last updated: Sep 14, 2023 |
Comment:
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: 15625830, … (more)
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: 15625830, 8935319, 23313052, 25440321, 20236109, 7390473, 29783823, 15766741, 7327562, 18270558, 11793482, 12497642, 15316963, 18046504, 34659341, 21931771, 29339739, 18329300, 24958328, 25775246, 26829728, 29702993, 29783822, 15223006, 17587269, 23006493, 15727905, 21874587, 16155737, 16331553, 16528451, 15476167, 17018380, 16513531, 16329560, 11295127, 16927025, 22938511, 14505231, 1953767, 9891846, 28376293, 31628766, 33069889, 32959227, 34953813, 36071769, 35611242, 29251006, 35193651, 35313968, 12215013, 34272389) (less)
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Pathogenic
(Oct 26, 2023)
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criteria provided, single submitter
Method: clinical testing
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Malaria, susceptibility to
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV004195386.1
First in ClinVar: Dec 30, 2023 Last updated: Dec 30, 2023 |
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Pathogenic
(Jan 19, 2024)
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criteria provided, single submitter
Method: clinical testing
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Anemia, nonspherocytic hemolytic, due to G6PD deficiency
Affected status: unknown
Allele origin:
germline
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Revvity Omics, Revvity
Accession: SCV002023787.3
First in ClinVar: Nov 29, 2021 Last updated: Feb 04, 2024 |
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Pathogenic
(Aug 04, 2022)
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criteria provided, single submitter
Method: clinical testing
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Anemia, nonspherocytic hemolytic, due to G6PD deficiency
Affected status: unknown
Allele origin:
germline
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Molecular Genetics, Royal Melbourne Hospital
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV004812458.1
First in ClinVar: Apr 15, 2024 Last updated: Apr 15, 2024 |
Comment:
This sequence change in G6PD is predicted to replace arginine with histidine at codon 463, p.(Arg463His). The arginine residue is highly conserved (100 vertebrates, UCSC), … (more)
This sequence change in G6PD is predicted to replace arginine with histidine at codon 463, p.(Arg463His). The arginine residue is highly conserved (100 vertebrates, UCSC), and is located in the C-terminal glucose-6-phosphate dehydrogenase domain. There is a small physicochemical difference between arginine and histidine. The highest population minor allele frequency in gnomAD v2.1 is 0.7% (104/14,782 alleles, 1 homozygote, 32 hemizygotes) in the East Asian population. This variant is the most common cause of glucose-6-phosphate dehydrogenase (G6PD) deficiency in China (also known as Kaiping). It has been detected in hemizygous in affected males and compound heterozygous with a second pathogenic variant or homozygous in affected females. Individuals with this variant display reduced G6PD activity in their cells, with female heterozygous carriers demonstrating moderate deficiency (PMID: 33051526). Multiple lines of computational evidence predict a deleterious effect for the missense substitution (6/6 algorithms). Based on the classification scheme RMH Modified ACMG Guidelines v1.5.1, this variant is classified as PATHOGENIC. Following criteria are met: PM3_VeryStrong, PP3, PP4. (less)
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Pathogenic
(May 01, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV001962678.15
First in ClinVar: Oct 08, 2021 Last updated: May 12, 2024 |
Comment:
G6PD: PS3, PM1, PP1:Moderate, PP3, PS4:Supporting
Number of individuals with the variant: 3
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Pathogenic
(Oct 01, 2021)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000603772.3
First in ClinVar: Sep 30, 2017 Last updated: Jan 08, 2022 |
Comment:
The G6PD c.1388G>A; p.Arg463His variant (rs72554664), also known as G6PD Kaiping, is reported in the literature as a common G6PD deficiency variant in Asian populations … (more)
The G6PD c.1388G>A; p.Arg463His variant (rs72554664), also known as G6PD Kaiping, is reported in the literature as a common G6PD deficiency variant in Asian populations (Chiu 1991, Fu 2018, Li 1998, Nuchprayoon 2002). This variant is reported in ClinVar (Variation ID: 100059), and is found in the East Asian population with an allele frequency of 0.70% (104/14782 alleles, including 32 hemizygotes and a single homozygote) in the Genome Aggregation Database. The arginine at codon 463 is highly conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. Additionally, other variants at this codon (c.1387C>T; p.Arg463Cys, c.1387C>A; p.Arg462Ser) have been reported in individuals with G6PD deficiency (Hirono 1997, Rodrigues 2002). Based on available information, the p.Arg463His variant is considered to be pathogenic. References: Chiu DT et al. Two commonly occurring nucleotide base substitutions in Chinese G6PD variants. Biochem Biophys Res Commun. 1991 180(2):988-93. Fu C et al. Newborn screening of glucose-6-phosphate dehydrogenase deficiency in Guangxi, China: determination of optimal cutoff value to identify heterozygous female neonates. Sci Rep. 2018 Jan 16;8(1):833. Hirono A et al. Molecular analysis of eight biochemically unique glucose-6-phosphate dehydrogenase variants found in Japan. Blood. 1997 Jun 15;89(12):4624-7. Li P et al. Analysis of common mutations and associated haplotypes in Chinese patients with glucose-6-phosphate dehydrogenase deficiency. Biochem Mol Biol Int. 1998 46(6):1135-43. Nuchprayoon I et al. Glucose-6-phosphate dehydrogenase (G6PD) mutations in Thailand: G6PD Viangchan (871G>A) is the most common deficiency variant in the Thai population. Hum Mutat. 2002 Feb;19(2):185. Rodrigues MO et al. Glucose-6-phosphate dehydrogenase deficiency in Portugal: biochemical and mutational profiles, heterogeneity, and haplotype association. Blood Cells Mol Dis. 2002 Mar-Apr;28(2):249-59. (less)
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Pathogenic
(Apr 25, 2023)
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criteria provided, single submitter
Method: clinical testing
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G6PD deficiency
Affected status: unknown
Allele origin:
unknown
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Illumina Laboratory Services, Illumina
Accession: SCV004014652.1
First in ClinVar: Jul 22, 2023 Last updated: Jul 22, 2023 |
Comment:
The G6PD c.1478G>A (p.Arg493His) variant, also known as c.1388G>A (p.Arg463His), or G6PD Kaiping, is a missense variant. In the literature, this variant is reported as … (more)
The G6PD c.1478G>A (p.Arg493His) variant, also known as c.1388G>A (p.Arg463His), or G6PD Kaiping, is a missense variant. In the literature, this variant is reported as one of the most common pathogenic variants associated with glucose-6-phosphate dehydrogenase deficiency in the East Asian population (PMID: 36949502; 33051526). The highest frequency of this allele in the Genome Aggregation Database is 0.007036 in the East Asian population (version 2.1.1). This frequency is high but is consistent with disease prevalence estimates. Multiple lines of computational evidence suggest the variant may impact the gene or gene product. This variant has been classified as pathogenic by at least twelve submitters in ClinVar. Based on the available evidence, the c.1478G>A (p.Arg493His) variant is classified as pathogenic for glucose-6-phosphate dehydrogenase deficiency. (less)
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Pathogenic
(Jan 19, 2024)
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criteria provided, single submitter
Method: clinical testing
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Anemia, nonspherocytic hemolytic, due to G6PD deficiency
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV000964252.6
First in ClinVar: Aug 14, 2019 Last updated: Feb 14, 2024 |
Comment:
This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 463 of the G6PD protein (p.Arg463His). … (more)
This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 463 of the G6PD protein (p.Arg463His). This variant is present in population databases (rs72554664, gnomAD 0.7%), and has an allele count higher than expected for a pathogenic variant. This variant has been described as a common cause of glucose-6-phosphate dehydrogenase deficiency in southeast Asia, although it has also been reported in affected individuals from other populations (PMID: 9589612, 30315739, 17726510, 21446359, 15906717, 15223006, 20236109). This variant is also known as Kaiping. ClinVar contains an entry for this variant (Variation ID: 100059). 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) performed at Invitae indicates that this missense variant is expected to disrupt G6PD protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic. (less)
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other
(May 24, 2017)
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no assertion criteria provided
Method: literature only
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G6PD KAIPING
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000031347.5
First in ClinVar: Apr 04, 2013 Last updated: May 27, 2017 |
Comment on evidence:
Zuo et al. (1990) demonstrated substitution of histidine for arginine-463 resulting from a G-to-A mutation in nucleotide 1388. The G6PD was of the WHO class … (more)
Zuo et al. (1990) demonstrated substitution of histidine for arginine-463 resulting from a G-to-A mutation in nucleotide 1388. The G6PD was of the WHO class 2. The Chinese variant G6PD Kaiping was discovered by Du et al. (1988). The same mutation was found in G6PD Anant (Panich and Sungnate, 1973), Dhon (Panich and Na-Nakorn, 1980), Petrich-like (Shatskaya et al., 1980), and Sapporo-like (Fujii et al., 1981). (less)
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other
(May 24, 2017)
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no assertion criteria provided
Method: literature only
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G6PD ANANT
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000031348.5
First in ClinVar: Apr 04, 2013 Last updated: May 27, 2017 |
Comment on evidence:
Zuo et al. (1990) demonstrated substitution of histidine for arginine-463 resulting from a G-to-A mutation in nucleotide 1388. The G6PD was of the WHO class … (more)
Zuo et al. (1990) demonstrated substitution of histidine for arginine-463 resulting from a G-to-A mutation in nucleotide 1388. The G6PD was of the WHO class 2. The Chinese variant G6PD Kaiping was discovered by Du et al. (1988). The same mutation was found in G6PD Anant (Panich and Sungnate, 1973), Dhon (Panich and Na-Nakorn, 1980), Petrich-like (Shatskaya et al., 1980), and Sapporo-like (Fujii et al., 1981). (less)
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other
(May 24, 2017)
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no assertion criteria provided
Method: literature only
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G6PD DHON
Affected status: not provided
Allele origin:
germline
|
OMIM
Accession: SCV000031349.5
First in ClinVar: Apr 04, 2013 Last updated: May 27, 2017 |
Comment on evidence:
Zuo et al. (1990) demonstrated substitution of histidine for arginine-463 resulting from a G-to-A mutation in nucleotide 1388. The G6PD was of the WHO class … (more)
Zuo et al. (1990) demonstrated substitution of histidine for arginine-463 resulting from a G-to-A mutation in nucleotide 1388. The G6PD was of the WHO class 2. The Chinese variant G6PD Kaiping was discovered by Du et al. (1988). The same mutation was found in G6PD Anant (Panich and Sungnate, 1973), Dhon (Panich and Na-Nakorn, 1980), Petrich-like (Shatskaya et al., 1980), and Sapporo-like (Fujii et al., 1981). (less)
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other
(May 24, 2017)
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no assertion criteria provided
Method: literature only
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G6PD PETRICH-LIKE
Affected status: not provided
Allele origin:
germline
|
OMIM
Accession: SCV000031350.5
First in ClinVar: Apr 04, 2013 Last updated: May 27, 2017 |
Comment on evidence:
Zuo et al. (1990) demonstrated substitution of histidine for arginine-463 resulting from a G-to-A mutation in nucleotide 1388. The G6PD was of the WHO class … (more)
Zuo et al. (1990) demonstrated substitution of histidine for arginine-463 resulting from a G-to-A mutation in nucleotide 1388. The G6PD was of the WHO class 2. The Chinese variant G6PD Kaiping was discovered by Du et al. (1988). The same mutation was found in G6PD Anant (Panich and Sungnate, 1973), Dhon (Panich and Na-Nakorn, 1980), Petrich-like (Shatskaya et al., 1980), and Sapporo-like (Fujii et al., 1981). (less)
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other
(May 24, 2017)
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no assertion criteria provided
Method: literature only
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G6PD SAPPORO-LIKE
Affected status: not provided
Allele origin:
germline
|
OMIM
Accession: SCV000031351.5
First in ClinVar: Apr 04, 2013 Last updated: May 27, 2017 |
Comment on evidence:
Zuo et al. (1990) demonstrated substitution of histidine for arginine-463 resulting from a G-to-A mutation in nucleotide 1388. The G6PD was of the WHO class … (more)
Zuo et al. (1990) demonstrated substitution of histidine for arginine-463 resulting from a G-to-A mutation in nucleotide 1388. The G6PD was of the WHO class 2. The Chinese variant G6PD Kaiping was discovered by Du et al. (1988). The same mutation was found in G6PD Anant (Panich and Sungnate, 1973), Dhon (Panich and Na-Nakorn, 1980), Petrich-like (Shatskaya et al., 1980), and Sapporo-like (Fujii et al., 1981). (less)
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Pathogenic
(Jan 06, 2020)
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no assertion criteria provided
Method: curation
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Glucose 6 phosphate dehydrogenase deficiency
Affected status: unknown
Allele origin:
germline
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Reproductive Health Research and Development, BGI Genomics
Accession: SCV001142503.1
First in ClinVar: Jan 12, 2020 Last updated: Jan 12, 2020 |
Comment:
NM_001042351.1:c.1388G>A in the G6PD gene has an allele frequency of 0.007 in East Asian subpopulation in the gnomAD database. This variant has been described as … (more)
NM_001042351.1:c.1388G>A in the G6PD gene has an allele frequency of 0.007 in East Asian subpopulation in the gnomAD database. This variant has been described as a common cause of glucose-6-phosphate dehydrogenase deficiency in Southeast Asia, although it has also been reported in affected individuals from other populations (PMID: 9589612, 30315739, 17726510, 21446359, 15906717, 15223006, 20236109). Experimental studies have shown that this missense change causes a significant reduction in enzyme activity and affinity for glucose-6-phosphate (PMID: 16607506). Pathogenic computational verdict because pathogenic predictions from DANN, DEOGEN2, FATHMM-MKL, M-CAP, MVP, MutationAssessor, MutationTaster, REVEL and SIFTT. aken together, we interprete this variant as Pathogenic/Likely pathogenic. ACMG/AMP Criteria applied: PS3; PS4; PP4. (less)
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Genotypic and phenotypic characterization of glucose-6-phosphate dehydrogenase (G6PD) deficiency in Guangzhou, China. | Li Z | Human genomics | 2023 | PMID: 36949502 |
Cut-off values for diagnosis of G6PD deficiency by flow cytometry in Thai population. | Thedsawad A | Annals of hematology | 2022 | PMID: 35840819 |
Combined effects of double mutations on catalytic activity and structural stability contribute to clinical manifestations of glucose-6-phosphate dehydrogenase deficiency. | Pakparnich P | Scientific reports | 2021 | PMID: 34934109 |
Glucose-6-phosphate dehydrogenase deficiency in the Han Chinese population: molecular characterization and genotype-phenotype association throughout an activity distribution. | He Y | Scientific reports | 2020 | PMID: 33051526 |
Fine Mapping of Glucose 6 Phosphate Dehydrogenase (G6PD) Deficiency in a Rural Malaria Area of South West Odisha Using the Clinical, Hematological and Molecular Approach. | Kumar R | Mediterranean journal of hematology and infectious diseases | 2020 | PMID: 32180910 |
Genotyping of Malaysian G6PD-deficient neonates by reverse dot blot flow-through hybridisation. | Alina MF | Journal of human genetics | 2020 | PMID: 31863082 |
Chinese newborn screening for the incidence of G6PD deficiency and variant of G6PD gene from 2013 to 2017. | Liu Z | Human mutation | 2020 | PMID: 31489982 |
G6PD genetic variations in neonatal Hyperbilirubinemia in Indonesian Deutromalay population. | Wisnumurti DA | BMC pediatrics | 2019 | PMID: 31862010 |
Analysis of Glucose-6-Phosphate Dehydrogenase Genetic Polymorphism in the Hakka Population in Southern China. | Zhong Z | Medical science monitor : international medical journal of experimental and clinical research | 2018 | PMID: 30315739 |
Mutation of glucose-6-phosphate dehydrogenase deficiency in Chinese Han children in eastern Fujian. | Chen Y | Medicine | 2018 | PMID: 30045279 |
Two new variants of G6PD deficiencies in Singapore. | Hamada M | Nepal Medical College journal : NMCJ | 2010 | PMID: 21446359 |
Genetics of glucose-6-phosphate dehydrogenase deficiency in Saudi patients. | Faiyaz-Ul-Haque M | Clinical genetics | 2010 | PMID: 20236109 |
The first case of a class I glucose-6-phosphate dehydrogenase deficiency, G6PD Santiago de Cuba (1339 G > A), in a Chinese population as found in a survey for G6PD deficiency in northeastern and central China. | Wang J | Acta medica Okayama | 2010 | PMID: 20200584 |
Glucose-6-phosphate dehydrogenase mutations in Mon and Burmese of southern Myanmar. | Nuchprayoon I | Journal of human genetics | 2008 | PMID: 18046504 |
Seven different glucose-6-phosphate dehydrogenase variants including a new variant distributed in Lam Dong Province in southern Vietnam. | Matsuoka H | Acta medica Okayama | 2007 | PMID: 17726510 |
Further investigations of glucose-6-phosphate dehydrogenase variants in Flores Island, eastern Indonesia. | Kawamoto F | Journal of human genetics | 2006 | PMID: 16927025 |
Structure and function of glucose-6-phosphate dehydrogenase-deficient variants in Chinese population. | Jiang W | Human genetics | 2006 | PMID: 16607506 |
Glucose-6-phosphate dehydrogenase variants associated with favism in Thai children. | Laosombat V | International journal of hematology | 2006 | PMID: 16513531 |
Detection of three common G6PD gene mutations in Chinese individuals by probe melting curves. | Zhang DT | Clinical biochemistry | 2005 | PMID: 15766741 |
Molecular heterogeneity of glucose-6-phosphate dehydrogenase (G6PD) variants in the south of Thailand and identification of a novel variant (G6PD Songklanagarind). | Laosombat V | Blood cells, molecules & diseases | 2005 | PMID: 15727905 |
Complete molecular characterisation of glucose-6-phosphate dehydrogenase (G6PD) deficiency in a group of Malaysian Chinese neonates. | Ainoon O | The Malaysian journal of pathology | 2004 | PMID: 16329560 |
Molecular characterization of G6PD deficiency in Cyprus. | Drousiotou A | Blood cells, molecules & diseases | 2004 | PMID: 15223006 |
G6PD Viangchan and G6PD Mediterranean are the main variants in G6PD deficiency in the Malay population of Malaysia. | Yusoff NM | The Southeast Asian journal of tropical medicine and public health | 2003 | PMID: 15906717 |
Glucose-6-phosphate dehydrogenase (G6PD) variants in Malaysian Malays. | Ainoon O | Human mutation | 2003 | PMID: 12497642 |
Glucose-6-phosphate dehydrogenase deficiency in Portugal: biochemical and mutational profiles, heterogeneity, and haplotype association. | Rodrigues MO | Blood cells, molecules & diseases | 2002 | PMID: 12064920 |
Glucose-6-phosphate dehydrogenase (G6PD) mutations in Thailand: G6PD Viangchan (871G>A) is the most common deficiency variant in the Thai population. | Nuchprayoon I | Human mutation | 2002 | PMID: 11793482 |
Glucose-6-phosphate dehydrogenase (G6PD) variants in Malaysian Chinese. | Ainoon O | Human mutation | 1999 | PMID: 10502785 |
Molecular characterization of Chinese G6PD deficiency by using polymerase chain reaction/single strand conformation polymorphism. | Chen BH | The Kaohsiung journal of medical sciences | 1998 | PMID: 9589612 |
Molecular analysis of eight biochemically unique glucose-6-phosphate dehydrogenase variants found in Japan. | Hirono A | Blood | 1997 | PMID: 9192788 |
Glucose-6 phosphate dehydrogenase mutations and haplotypes in various ethnic groups. | Xu W | Blood | 1995 | PMID: 7803800 |
Biochemical characteristics of four common molecular variants in glucose-6-phosphate dehydrogenase-deficient Chinese in Singapore. | Saha N | Human heredity | 1995 | PMID: 7590755 |
Molecular characterization of glucose-6-phosphate dehydrogenase (G6PD) deficiency in patients of Chinese descent and identification of new base substitutions in the human G6PD gene. | Chiu DT | Blood | 1993 | PMID: 8471773 |
Frequency of glucose-6-phosphate dehydrogenase (G6PD) mutations in Chinese, Filipinos, and Laotians from Hawaii. | Hsia YE | Human genetics | 1993 | PMID: 8244337 |
Glucose-6-phosphate dehydrogenase variants in Hawaii. | Beutler E | Human heredity | 1992 | PMID: 1459579 |
Two commonly occurring nucleotide base substitutions in Chinese G6PD variants. | Chiu DT | Biochemical and biophysical research communications | 1991 | PMID: 1953767 |
Glucose-6-phosphate dehydrogenase variants and their frequency in Guangdong, China. | Du CS | Human genetics | 1988 | PMID: 3198117 |
Glucose 6-phosphate dehydrogenase variants: a unique variant (G6PD Kobe) showed an extremely increased affinity for galactose 6-phosphate and a new variant (G6PD Sapporo) resembling G6PD Pea Ridge. | Fujii H | Human genetics | 1981 | PMID: 7327562 |
Variants of erythrocyte glucose-6-phosphate dehydrogenase (G6PD) in Bulgarian populations. | Shatskaya TL | Human genetics | 1980 | PMID: 7390473 |
G-6-PD Intanon. A new glucose-6-phosphate dehydrogenase variant. | Panich V | Humangenetik | 1974 | PMID: 4837298 |
Characterization of glucose-6-phosphate dehydrogenase in Thailand. The occurrence of 6 variants among 50 G-6-PD deficient Thai. | Panich V | Humangenetik | 1973 | PMID: 4721339 |
Du, C.-S., Hua, X.-Y., Wu, Q.-L., Li, C.-Q., Zheng, J.-F., Li, H.-L. Studies on erythrocyte glucose-6-phosphate dehydrogenase variants in Chinese. IV. Gd(-) Gaohe associated with paroxysmal nocturnal hemoglobinuria. Chinese J. Pathophysiol. 1: 12-15, 1985. | - | - | - | - |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=G6PD | - | - | - | - |
Panich, V. G6PD characterization in Thailand. Genetics 74 (suppl.): s208-only, 1973. | - | - | - | - |
Zuo, L., Chen, E., Du, C. S., Chang, C. N., Chiu, D. T. Y. Genetic study of Chinese G6PD variants by direct PCR sequencing. (Abstract) Blood 76 (suppl. 1): 51A, 1990. | - | - | - | - |
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Text-mined citations for rs72554664 ...
HelpRecord last updated May 27, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.