NM_000169.3(GLA):c.758TTG[1] (p.Val254del) AND Fabry disease

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 19, 2022
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:: RCV003050637.4

Allele description [Variation Report for NM_000169.3(GLA):c.758TTG[1] (p.Val254del)]

NM_000169.3(GLA):c.758TTG[1] (p.Val254del)

Genes:

RPL36A-HNRNPH2:RPL36A-HNRNPH2 readthrough [Gene - HGNC]
GLA:galactosidase alpha [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

Xq22.1

Genomic location:

Preferred name:

NM_000169.3(GLA):c.758TTG[1] (p.Val254del)

HGVS:

NC_000023.11:g.101398823CAA[1]
NG_007119.1:g.14136TTG[1]
NM_000169.3:c.758TTG[1]MANE SELECT
NM_001199973.2:c.300+3369_300+3371del
NM_001199974.2:c.177+7004_177+7006del
NM_001406747.1:c.881TTG[1]
NM_001406748.1:c.758TTG[1]
NP_000160.1:p.Val254del
NP_000160.1:p.Val254del
NP_001393676.1:p.Val295del
NP_001393677.1:p.Val254del
LRG_672t1:c.758_760TTG[1]
LRG_672:g.14136TTG[1]
LRG_672p1:p.Val254del
NC_000023.10:g.100653811CAA[1]
NC_000023.10:g.100653811_100653813del
NM_000169.2:c.758_760TTG[1]
NR_164783.1:n.837TTG[1]
NR_176252.1:n.688TTG[1]
NR_176253.1:n.895TTG[1]

Protein change:

V254del

Molecular consequence:

NM_000169.3:c.758TTG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406747.1:c.881TTG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001406748.1:c.758TTG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001199973.2:c.300+3369_300+3371del - intron variant - [Sequence Ontology: SO:0001627]
NM_001199974.2:c.177+7004_177+7006del - intron variant - [Sequence Ontology: SO:0001627]
NR_164783.1:n.837TTG[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176252.1:n.688TTG[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176253.1:n.895TTG[1] - 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
SCV003445107	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 19, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 16189631, 33016649, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003445107

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 19, 2022)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

Significance of screening for Fabry disease among male dialysis patients.

Ichinose M, Nakayama M, Ohashi T, Utsunomiya Y, Kobayashi M, Eto Y.

Clin Exp Nephrol. 2005 Sep;9(3):228-32.

PubMed [citation]

PMID:: 16189631

Detection of novel Fabry disease-associated pathogenic variants in Japanese patients by newborn and high-risk screening.

Sawada T, Kido J, Sugawara K, Matsumoto S, Takada F, Tsuboi K, Ohtake A, Endo F, Nakamura K.

Mol Genet Genomic Med. 2020 Nov;8(11):e1502. doi: 10.1002/mgg3.1502. Epub 2020 Oct 5.

PubMed [citation]

PMID:: 33016649
PMCID:: PMC7667298

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003445107.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant is also known as 10252_10254 del 3, c.758_760delTTG. This variant has been observed in individual(s) with clinical features of Fabry disease (PMID: 16189631, 33016649). This variant is not present in population databases (gnomAD no frequency). This variant, c.761_763del, results in the deletion of 1 amino acid(s) of the GLA protein (p.Val254del), but otherwise preserves the integrity of the reading frame.

#	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 29, 2024

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