NM_000169.3(GLA):c.878C>T (p.Pro293Leu) AND Fabry disease

Germline classification:: Likely pathogenic (1 submission)
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:: RCV001391121.2

Allele description [Variation Report for NM_000169.3(GLA):c.878C>T (p.Pro293Leu)]

NM_000169.3(GLA):c.878C>T (p.Pro293Leu)

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.878C>T (p.Pro293Leu)

HGVS:

NC_000023.11:g.101398491G>A
NG_007119.1:g.14473C>T
NM_000169.3:c.878C>TMANE SELECT
NM_001199973.2:c.300+3034G>A
NM_001199974.2:c.177+6669G>A
NM_001406747.1:c.1001C>T
NM_001406748.1:c.878C>T
NP_000160.1:p.Pro293Leu
NP_000160.1:p.Pro293Leu
NP_001393676.1:p.Pro334Leu
NP_001393677.1:p.Pro293Leu
LRG_672t1:c.878C>T
LRG_672:g.14473C>T
LRG_672p1:p.Pro293Leu
NC_000023.10:g.100653479G>A
NM_000169.2:c.878C>T
NR_164783.1:n.957C>T
NR_176252.1:n.808C>T
NR_176253.1:n.1015C>T

Protein change:

P293L

Links:

dbSNP: rs869312441

NCBI 1000 Genomes Browser:

rs869312441

Molecular consequence:

NM_001199973.2:c.300+3034G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001199974.2:c.177+6669G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000169.3:c.878C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406747.1:c.1001C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406748.1:c.878C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_164783.1:n.957C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176252.1:n.808C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176253.1:n.1015C>T - 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
SCV001593026	Precision Medicine Center, Zhengzhou University	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	germline	research	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001593026

Precision Medicine Center, Zhengzhou University

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic

germline

research

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	yes	not provided	not provided	not provided	not provided	not provided	research

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 Precision Medicine Center, Zhengzhou University, SCV001593026.1

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

Description

PM1:Located in a mutational hot spot PM2:not found in gnomAD PP2:Missense variant in a gene that has a low rate of benign missense variation and in which missense variants are a common mechanism of disease PP3:Multiple lines of computational evidence support a deleterious effect on the gene or gene product PP4:Patient's phenotype is highly specific for a disease

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

Last Updated: Sep 16, 2024

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