NM_000169.3(GLA):c.181G>A (p.Asp61Asn) AND Fabry disease

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 17, 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:: RCV001176589.5

Allele description [Variation Report for NM_000169.3(GLA):c.181G>A (p.Asp61Asn)]

NM_000169.3(GLA):c.181G>A (p.Asp61Asn)

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.181G>A (p.Asp61Asn)

HGVS:

NC_000023.11:g.101407723C>T
NG_007119.1:g.5241G>A
NG_016327.1:g.4521C>T
NM_000169.3:c.181G>AMANE SELECT
NM_001199973.2:c.301-4213C>T
NM_001199974.2:c.178-4213C>T
NM_001406747.1:c.181G>A
NM_001406748.1:c.181G>A
NM_001406749.1:c.181G>A
NP_000160.1:p.Asp61Asn
NP_000160.1:p.Asp61Asn
NP_001393676.1:p.Asp61Asn
NP_001393677.1:p.Asp61Asn
NP_001393678.1:p.Asp61Asn
LRG_672t1:c.181G>A
LRG_672:g.5241G>A
LRG_672p1:p.Asp61Asn
NC_000023.10:g.100662711C>T
NM_000169.2:c.181G>A
NR_164783.1:n.203G>A
NR_176252.1:n.203G>A
NR_176253.1:n.203G>A

Protein change:

D61N

Links:

dbSNP: rs1928578650

NCBI 1000 Genomes Browser:

rs1928578650

Molecular consequence:

NM_001199973.2:c.301-4213C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001199974.2:c.178-4213C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_000169.3:c.181G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406747.1:c.181G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406748.1:c.181G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406749.1:c.181G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_164783.1:n.203G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176252.1:n.203G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176253.1:n.203G>A - 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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001340612	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Sep 17, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001340612

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Sep 17, 2019)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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 Color Diagnostics, LLC DBA Color Health, SCV001340612.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This missense variant replaces aspartic acid with asparagine at codon 61 of the GLA protein. Computational prediction tool suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold ≤0.5, PMID: 27666373). Splice site prediction tools suggest that this variant may not impact RNA splicing. To our knowledge, functional studies have not been performed for this variant. This variant has not been reported in individuals affected with cardiovascular disorders in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 16, 2024

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