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NM_001360016.2(G6PD):c.1360C>T (p.Arg454Cys)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
10 (Most recent: Nov 19, 2021)
Last evaluated:
Oct 13, 2020
Accession:
VCV000093493.21
Variation ID:
93493
Description:
single nucleotide variant
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NM_001360016.2(G6PD):c.1360C>T (p.Arg454Cys)

Allele ID
99398
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
Xq28
Genomic location
X: 154532390 (GRCh38) GRCh38 UCSC
X: 153760605 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000023.10:g.153760605G>A
NC_000023.11:g.154532390G>A
NG_009015.2:g.20183C>T
... more HGVS
Protein change
R454C, R484C
Other names
-
Canonical SPDI
NC_000023.11:154532389:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00053 (A)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00014
Exome Aggregation Consortium (ExAC) 0.00011
1000 Genomes Project 0.00053
The Genome Aggregation Database (gnomAD) 0.00009
The Genome Aggregation Database (gnomAD), exomes 0.00015
Trans-Omics for Precision Medicine (TOPMed) 0.00015
Links
ClinGen: CA200806
dbSNP: rs398123546
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 5 criteria provided, multiple submitters, no conflicts May 3, 2020 RCV000079396.13
Pathogenic 3 criteria provided, multiple submitters, no conflicts Oct 13, 2020 RCV000174032.11
Pathogenic 1 criteria provided, single submitter Mar 27, 2020 RCV000507961.4
Pathogenic 1 criteria provided, single submitter Sep 20, 2018 RCV000778894.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
G6PD - - GRCh38
GRCh37
223 462

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Oct 06, 2014)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000281545.1
Submitted: (May 19, 2016)
Evidence details
Pathogenic
(Oct 29, 2013)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000225263.5
Submitted: (Jun 30, 2017)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Pathogenic
(Mar 27, 2020)
criteria provided, single submitter
Method: clinical testing
none provided
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000603769.3
Submitted: (Dec 11, 2020)
Evidence details
Comment:
The G6PD c.1360C>T; p.Arg454Cys variant (rs398123546), also known as the Union or Maewo variant, has been described in the literature in individuals with severe G6PD … (more)
Pathogenic
(Oct 13, 2020)
criteria provided, single submitter
Method: clinical testing
Anemia, nonspherocytic hemolytic, due to G6PD deficiency
Allele origin: germline
Invitae
Accession: SCV000647799.6
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (6)
Comment:
This sequence change replaces arginine with cysteine at codon 454 of the G6PD protein (p.Arg454Cys). The arginine residue is highly conserved and there is a … (more)
Pathogenic
(Sep 20, 2018)
criteria provided, single submitter
Method: clinical testing
Glucose 6 phosphate dehydrogenase deficiency
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000915297.1
Submitted: (Feb 01, 2019)
Evidence details
Publications
PubMed (3)
Comment:
Across a selection of literature, the G6PD c.1360C>T (p.Arg454Cys) variant has been reported in at least two studies and is found in a total of … (more)
Pathogenic
(Oct 03, 2018)
criteria provided, single submitter
Method: clinical testing
ANEMIA, NONSPHEROCYTIC HEMOLYTIC, DUE TO G6PD DEFICIENCY
Allele origin: germline
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego
Accession: SCV000996202.1
Submitted: (Sep 20, 2019)
Evidence details
Comment:
This variant is also known in the literature as c.1360C>T (p.Arg454Cys) and is also commonly described as the "Union" or "Maewo" variant. In the gnomAD … (more)
Pathogenic
(May 03, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: unknown
Genomic Research Center,Shahid Beheshti University of Medical Sciences
Accession: SCV001251668.1
Submitted: (May 03, 2020)
Evidence details
Pathogenic
(Dec 04, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001830638.1
Submitted: (Sep 03, 2021)
Evidence details
Comment:
Published functional studies demonstrate a damaging effect by significantly decreasing the kinetic behavior and thermostability of the protein (Wang et al., 2005); This variant is … (more)
Pathogenic
(Jun 01, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001248070.6
Submitted: (Jul 04, 2021)
Evidence details
Pathogenic
(Jul 22, 2019)
no assertion criteria provided
Method: clinical testing
Anemia, nonspherocytic hemolytic, due to G6PD deficiency
Allele origin: germline
PerkinElmer Genomics
Accession: SCV002023783.1
Submitted: (Nov 19, 2021)
Evidence details

Functional evidence

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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 this variant

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Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Molecular epidemiological investigation of G6PD deficiency by a gene chip among Chinese Hakka of southern Jiangxi province. Hu R International journal of clinical and experimental pathology 2015 PMID: 26823837
Glucose-6-phosphate dehydrogenase (G6PD) mutations database: review of the "old" and update of the new mutations. Minucci A Blood cells, molecules & diseases 2012 PMID: 22293322
Marked decrease in specific activity contributes to disease phenotype in two human glucose 6-phosphate dehydrogenase mutants, G6PD(Union) and G6PD(Andalus). Wang XT Human mutation 2005 PMID: 16088936
Glucose-6-phosphate dehydrogenase (G6PD) variants in Malaysian Malays. Ainoon O Human mutation 2003 PMID: 12497642
Molecular basis of glucose-6-phosphate dehydrogenase deficiency among Filipinos. Silao CL Pediatrics international : official journal of the Japan Pediatric Society 1999 PMID: 10221015
Multiple glucose 6-phosphate dehydrogenase-deficient variants correlate with malaria endemicity in the Vanuatu archipelago (southwestern Pacific). Ganczakowski M American journal of human genetics 1995 PMID: 7825590
Genetic heterogeneity of glucose-6-phosphate dehydrogenase deficiency revealed by single-strand conformation and sequence analysis. Calabrò V American journal of human genetics 1993 PMID: 8447319
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=G6PD - - - -

Text-mined citations for rs398123546...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 28, 2021