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NM_000169.3(GLA):c.994del (p.Arg332fs) AND GLA-related disorder

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Feb 16, 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:
RCV003983408.2

Allele description [Variation Report for NM_000169.3(GLA):c.994del (p.Arg332fs)]

NM_000169.3(GLA):c.994del (p.Arg332fs)

Genes:
RPL36A-HNRNPH2:RPL36A-HNRNPH2 readthrough [Gene - HGNC]
GLA:galactosidase alpha [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
Xq22.1
Genomic location:
Preferred name:
NM_000169.3(GLA):c.994del (p.Arg332fs)
HGVS:
  • NC_000023.11:g.101398375del
  • NG_007119.1:g.14589del
  • NM_000169.3:c.994delMANE SELECT
  • NM_001199973.2:c.300+2918del
  • NM_001199974.2:c.177+6553del
  • NM_001406747.1:c.1117del
  • NM_001406748.1:c.994del
  • NP_000160.1:p.Arg332Aspfs
  • NP_000160.1:p.Arg332fs
  • NP_001393676.1:p.Arg373fs
  • NP_001393677.1:p.Arg332fs
  • LRG_672t1:c.994del
  • LRG_672:g.14589del
  • LRG_672p1:p.Arg332Aspfs
  • NC_000023.10:g.100653363del
  • NM_000169.2:c.994delA
  • NR_164783.1:n.1073del
  • NR_176252.1:n.924del
  • NR_176253.1:n.1131del
  • p.R332Dfs*16
Protein change:
R332fs
Links:
dbSNP: rs869312458
NCBI 1000 Genomes Browser:
rs869312458
Molecular consequence:
  • NM_000169.3:c.994del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406747.1:c.1117del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406748.1:c.994del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001199973.2:c.300+2918del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001199974.2:c.177+6553del - intron variant - [Sequence Ontology: SO:0001627]
  • NR_164783.1:n.1073del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176252.1:n.924del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176253.1:n.1131del - 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
SCV004800387PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Likely pathogenic
(Feb 16, 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, SCV004800387.2

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

Description

The GLA c.994delA variant is predicted to result in a frameshift and premature protein termination (p.Arg332Aspfs*16). This variant was reported in an individual with Fabry disease (Table 2, Germain et al 2002. PubMed ID: 12428061). This variant has not been reported in a large population database, indicating this variant is rare. Frameshift variants in GLA are expected to be pathogenic. Upstream and downstream loss-of-function variants have been described to be causative for Fabry disease. This variant is interpreted as likely pathogenic.

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

Last Updated: Oct 13, 2024