U.S. flag

An official website of the United States government

NM_000175.5(GPI):c.1414C>T (p.Arg472Cys) AND Hemolytic anemia due to glucophosphate isomerase deficiency

Germline classification:
Pathogenic (1 submission)
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001823208.4

Allele description [Variation Report for NM_000175.5(GPI):c.1414C>T (p.Arg472Cys)]

NM_000175.5(GPI):c.1414C>T (p.Arg472Cys)

Gene:
GPI:glucose-6-phosphate isomerase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19q13.11
Genomic location:
Preferred name:
NM_000175.5(GPI):c.1414C>T (p.Arg472Cys)
HGVS:
  • NC_000019.10:g.34399571C>T
  • NG_012838.3:g.44980C>T
  • NM_000175.5:c.1414C>TMANE SELECT
  • NM_001184722.1:c.1447C>T
  • NM_001289789.1:c.1531C>T
  • NM_001289790.3:c.1330C>T
  • NM_001329909.1:c.1414C>T
  • NM_001329910.1:c.1414C>T
  • NM_001329911.2:c.1387C>T
  • NP_000166.2:p.Arg472Cys
  • NP_001171651.1:p.Arg483Cys
  • NP_001276718.1:p.Arg511Cys
  • NP_001276719.1:p.Arg444Cys
  • NP_001316838.1:p.Arg472Cys
  • NP_001316839.1:p.Arg472Cys
  • NP_001316840.1:p.Arg463Cys
  • LRG_1178t1:c.1414C>T
  • LRG_1178:g.44980C>T
  • LRG_1178p1:p.Arg472Cys
  • NC_000019.9:g.34890476C>T
  • NM_000175.4:c.[1414C>T]
Protein change:
R444C
Links:
dbSNP: rs1364382189
NCBI 1000 Genomes Browser:
rs1364382189
Molecular consequence:
  • NM_000175.5:c.1414C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001184722.1:c.1447C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001289789.1:c.1531C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001289790.3:c.1330C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001329909.1:c.1414C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001329910.1:c.1414C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001329911.2:c.1387C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hemolytic anemia due to glucophosphate isomerase deficiency (CNSHA4)
Synonyms:
Hemolytic anemia, nonspherocytic, due to glucose phosphate isomerase deficiency; ANEMIA, CONGENITAL, NONSPHEROCYTIC HEMOLYTIC, 4
Identifiers:
MONDO: MONDO:0013275; MedGen: C3150730; Orphanet: 712; OMIM: 613470

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002073105Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenicgermlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Neuberg Centre For Genomic Medicine, NCGM, SCV002073105.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The missense variant p.R472C in GPI (NM_000175.5) has been previously reported in both homozygous as well as compound heterozygous state (Mojzikova R et al).Functional studies in the same patients showed decreased thermal stability as well as decreased affinity. The p.R472C variant is novel (not in any individuals) in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. The p.R472C missense variant is predicted to be damaging by both SIFT and PolyPhen2. The arginine residue at codon 472 of GPI is conserved in all mammalian species.The nucleotide c.1414 in GPI is predicted conserved by GERP++ and PhyloP across 100 vertebrates.For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 20, 2024