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NM_000169.3(GLA):c.307G>T (p.Glu103Ter) AND Fabry disease

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 9, 2018
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:
RCV000781429.2

Allele description [Variation Report for NM_000169.3(GLA):c.307G>T (p.Glu103Ter)]

NM_000169.3(GLA):c.307G>T (p.Glu103Ter)

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.307G>T (p.Glu103Ter)
HGVS:
  • NC_000023.11:g.101403873C>A
  • NG_007119.1:g.9091G>T
  • NG_016327.1:g.671C>A
  • NM_000169.3:c.307G>TMANE SELECT
  • NM_001199973.2:c.301-8063C>A
  • NM_001199974.2:c.178-8063C>A
  • NP_000160.1:p.Glu103Ter
  • NP_000160.1:p.Glu103Ter
  • LRG_672t1:c.307G>T
  • LRG_672:g.9091G>T
  • LRG_672p1:p.Glu103Ter
  • NC_000023.10:g.100658861C>A
  • NM_000169.2:c.307G>T
  • NR_164783.1:n.329G>T
Protein change:
E103*
Links:
dbSNP: rs1569304851
NCBI 1000 Genomes Browser:
rs1569304851
Molecular consequence:
  • NM_001199973.2:c.301-8063C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001199974.2:c.178-8063C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NR_164783.1:n.329G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000169.3:c.307G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Fabry disease
Synonyms:
Angiokeratoma, diffuse; Anderson-Fabry disease; Hereditary dystopic lipidosis; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010526; MedGen: C0002986; Orphanet: 324; OMIM: 301500; Human Phenotype Ontology: HP:0001071

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000919447Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Pathogenic
(Oct 9, 2018) 		germlineclinical testing

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

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Functional characterisation of alpha-galactosidase a mutations as a basis for a new classification system in fabry disease.

Lukas J, Giese AK, Markoff A, Grittner U, Kolodny E, Mascher H, Lackner KJ, Meyer W, Wree P, Saviouk V, Rolfs A.

PLoS Genet. 2013;9(8):e1003632. doi: 10.1371/journal.pgen.1003632. Epub 2013 Aug 1.

PubMed [citation]
PMID:
23935525
PMCID:
PMC3731228

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000919447.1

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

Description

Variant summary: GLA c.307G>T (p.Glu103X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory (eg. p.Trp162X, p.Arg220X, p.Arg227X). The variant was absent in 178768 control chromosomes. c.307G>T has been reported in the literature in an individual affected with Fabry Disease and functional assays show the variant to have an enzyme activity of 0% compared to WT (Lukas_2013). No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as pathogenic.

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

Last Updated: Apr 15, 2024