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NM_000290.4(PGAM2):c.233G>A (p.Trp78Ter) AND PGAM2-related condition

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 22, 2023
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:
RCV003944788.1

Allele description [Variation Report for NM_000290.4(PGAM2):c.233G>A (p.Trp78Ter)]

NM_000290.4(PGAM2):c.233G>A (p.Trp78Ter)

Genes:
LOC129998343:ATAC-STARR-seq lymphoblastoid active region 25926 [Gene]
DBNL:drebrin like [Gene - OMIM - HGNC]
PGAM2:phosphoglycerate mutase 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7p13
Genomic location:
Preferred name:
NM_000290.4(PGAM2):c.233G>A (p.Trp78Ter)
HGVS:
  • NC_000007.14:g.44065297C>T
  • NG_013016.1:g.5291G>A
  • NM_000290.4:c.233G>AMANE SELECT
  • NM_001014436.3:c.*4381C>TMANE SELECT
  • NM_001122956.2:c.*4381C>T
  • NM_001284313.2:c.*4381C>T
  • NM_001362723.2:c.*4381C>T
  • NM_014063.7:c.*4381C>T
  • NP_000281.2:p.Trp78Ter
  • NC_000007.13:g.44104896C>T
  • NM_000290.3:c.233G>A
  • p.Trp78*
Protein change:
W78*; TRP78TER
Links:
OMIM: 612931.0001; dbSNP: rs10250779
NCBI 1000 Genomes Browser:
rs10250779
Molecular consequence:
  • NM_001014436.3:c.*4381C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001122956.2:c.*4381C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001284313.2:c.*4381C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001362723.2:c.*4381C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_014063.7:c.*4381C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_000290.4:c.233G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
PGAM2-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004770225PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Nov 22, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot 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 PreventionGenetics, part of Exact Sciences, SCV004770225.1

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

Description

The PGAM2 c.233G>A variant is predicted to result in premature protein termination (p.Trp78*). This is the most commonly reported causative variant in patients with phosphoglycerate mutase enzyme deficiency (Tsujino et al. 1993. PubMed ID: 8447317; Salameh et al. 2013. PubMed ID: 23169535; Koo and Oskarsson. 2016. PubMed ID: 27612597). This variant has been reported primarily in patients of African descent, which is consistent with the relatively high minor allele frequency in this population in gnomAD. This variant is interpreted as pathogenic.

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

Last Updated: Mar 16, 2024