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NM_000169.3(GLA):c.124A>G (p.Met42Val) AND GLA-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 12, 2024
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV003907777.2

Allele description [Variation Report for NM_000169.3(GLA):c.124A>G (p.Met42Val)]

NM_000169.3(GLA):c.124A>G (p.Met42Val)

Genes:
RPL36A-HNRNPH2:RPL36A-HNRNPH2 readthrough [Gene - HGNC]
GLA:galactosidase alpha [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq22.1
Genomic location:
Preferred name:
NM_000169.3(GLA):c.124A>G (p.Met42Val)
HGVS:
  • NC_000023.11:g.101407780T>C
  • NG_007119.1:g.5184A>G
  • NG_016327.1:g.4578T>C
  • NM_000169.3:c.124A>GMANE SELECT
  • NM_001199973.2:c.301-4156T>C
  • NM_001199974.2:c.178-4156T>C
  • NM_001406747.1:c.124A>G
  • NM_001406748.1:c.124A>G
  • NM_001406749.1:c.124A>G
  • NP_000160.1:p.Met42Val
  • NP_000160.1:p.Met42Val
  • NP_001393676.1:p.Met42Val
  • NP_001393677.1:p.Met42Val
  • NP_001393678.1:p.Met42Val
  • LRG_672t1:c.124A>G
  • LRG_672:g.5184A>G
  • LRG_672p1:p.Met42Val
  • NC_000023.10:g.100662768T>C
  • NM_000169.2:c.124A>G
  • NR_164783.1:n.146A>G
  • NR_176252.1:n.146A>G
  • NR_176253.1:n.146A>G
  • p.M42V
Protein change:
M42V
Links:
dbSNP: rs797044613
NCBI 1000 Genomes Browser:
rs797044613
Molecular consequence:
  • NM_001199973.2:c.301-4156T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001199974.2:c.178-4156T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000169.3:c.124A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406747.1:c.124A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406748.1:c.124A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406749.1:c.124A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NR_164783.1:n.146A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176252.1:n.146A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176253.1:n.146A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
GLA-related disorder
Synonyms:
GLA-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004724136PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Pathogenic
(Jan 12, 2024) 		germlineclinical testing

Help

Summary from all submissions

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

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004724136.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The GLA c.124A>G variant is predicted to result in the amino acid substitution p.Met42Val. This variant was reported in individuals with Fabry disease (Davies et al. 1996. PubMed ID: 8875188; Shimotori et al. 2008. PubMed ID: 18205205; Park et al. 2009. PubMed ID: 19287194) and in high-risk screening for Fabry disease (Yoshida et al. 2020. PubMed ID: 32843101). This variant has not been reported in a large population database, indicating this variant is rare. In vitro experimental studies suggest this variant impacts protein function (Lukas et al. 2013. PubMed ID: 23935525; Park et al. 2009. PubMed ID: 19287194; Shimotori et al. 2008. PubMed ID: 18205205). Alternate nucleotide changes affecting the same amino acid (p.Met42Leu; p.Met42Thr; p.Met42Arg; p.Met42Ile), have been reported in individuals with Fabry disease (Rosenthal et al. 2004. PubMed ID: 15492942; Shabbeer et al. 2002. PubMed ID: 12175777; Riera et al. 2015. PubMed ID: 25382311; Pan et al. 2016. PubMed ID: 27560961). This variant is interpreted as pathogenic.

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

Last Updated: Apr 13, 2025