U.S. flag

An official website of the United States government

NM_000169.3(GLA):c.620_630delinsCACT (p.Tyr207fs) AND Fabry disease

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Aug 6, 2019
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:
RCV001193071.2

Allele description [Variation Report for NM_000169.3(GLA):c.620_630delinsCACT (p.Tyr207fs)]

NM_000169.3(GLA):c.620_630delinsCACT (p.Tyr207fs)

Genes:
RPL36A-HNRNPH2:RPL36A-HNRNPH2 readthrough [Gene - HGNC]
GLA:galactosidase alpha [Gene - OMIM - HGNC]
Variant type:
Indel
Cytogenetic location:
Xq22.1
Genomic location:
Preferred name:
NM_000169.3(GLA):c.620_630delinsCACT (p.Tyr207fs)
HGVS:
  • NC_000023.11:g.101400675_101400685delinsAGTG
  • NG_007119.1:g.12279_12289delinsCACT
  • NM_000169.3:c.620_630delinsCACTMANE SELECT
  • NM_001199973.2:c.300+5218_300+5228delinsAGTG
  • NM_001199974.2:c.177+8853_177+8863delinsAGTG
  • NM_001406747.1:c.743_753delinsCACT
  • NM_001406748.1:c.620_630delinsCACT
  • NP_000160.1:p.Tyr207Serfs
  • NP_000160.1:p.Tyr207fs
  • NP_001393676.1:p.Tyr248fs
  • NP_001393677.1:p.Tyr207fs
  • LRG_672t1:c.620_630delinsCACT
  • LRG_672:g.12279_12289delinsCACT
  • NC_000023.10:g.100655663_100655673delinsAGTG
  • NM_000169.2:c.620_630delATATGTGGCCCinsCACT
  • NM_000169.2:c.620_630delinsCACT
  • NR_164783.1:n.642_652delinsCACT
  • NR_176253.1:n.757_767delinsCACT
Protein change:
Y207fs
Links:
dbSNP: rs1928279286
NCBI 1000 Genomes Browser:
rs1928279286
Molecular consequence:
  • NM_000169.3:c.620_630delinsCACT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406747.1:c.743_753delinsCACT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406748.1:c.620_630delinsCACT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001199973.2:c.300+5218_300+5228delinsAGTG - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001199974.2:c.177+8853_177+8863delinsAGTG - intron variant - [Sequence Ontology: SO:0001627]
  • NR_164783.1:n.642_652delinsCACT - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176253.1:n.757_767delinsCACT - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001361653Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Likely pathogenic
(Aug 6, 2019)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001361653.1

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

Description

Variant summary: GLA c.620_630delinsCACT (p.Tyr207SerfsX31) 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. The variant was absent in 179766 control chromosomes (gnomAD). To our knowledge, no occurrence of c.620_630delinsCACT in individuals affected with Fabry Disease and no experimental evidence demonstrating its impact on protein function have been reported. 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 likely pathogenic.

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

Last Updated: Sep 16, 2024