NM_000169.3(GLA):c.946_947insACGACACATCAGCCCTCAAGCCAAAGCTCTCCTTCAGGATAAGGACG (p.Val316fs) AND Fabry disease

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 28, 2021
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:: RCV001754537.2

Allele description [Variation Report for NM_000169.3(GLA):c.946_947insACGACACATCAGCCCTCAAGCCAAAGCTCTCCTTCAGGATAAGGACG (p.Val316fs)]

NM_000169.3(GLA):c.946_947insACGACACATCAGCCCTCAAGCCAAAGCTCTCCTTCAGGATAAGGACG (p.Val316fs)

Genes:

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

Variant type:

Insertion

Cytogenetic location:

Xq22.1

Genomic location:

Preferred name:

NM_000169.3(GLA):c.946_947insACGACACATCAGCCCTCAAGCCAAAGCTCTCCTTCAGGATAAGGACG (p.Val316fs)

HGVS:

NC_000023.11:g.101398468_101398469insTCGTCCTTATCCTGAAGGAGAGCTTTGGCTTGAGGGCTGATGTGTCG
NG_007119.1:g.14541_14542insACGACACATCAGCCCTCAAGCCAAAGCTCTCCTTCAGGATAAGGACG
NM_000169.3:c.946_947insACGACACATCAGCCCTCAAGCCAAAGCTCTCCTTCAGGATAAGGACGMANE SELECT
NM_001199973.2:c.300+3011_300+3012insTCGTCCTTATCCTGAAGGAGAGCTTTGGCTTGAGGGCTGATGTGTCG
NM_001199974.2:c.177+6646_177+6647insTCGTCCTTATCCTGAAGGAGAGCTTTGGCTTGAGGGCTGATGTGTCG
NM_001406747.1:c.1069_1070insACGACACATCAGCCCTCAAGCCAAAGCTCTCCTTCAGGATAAGGACG
NM_001406748.1:c.946_947insACGACACATCAGCCCTCAAGCCAAAGCTCTCCTTCAGGATAAGGACG
NP_000160.1:p.Val316Aspfs
NP_000160.1:p.Val316fs
NP_001393676.1:p.Val357fs
NP_001393677.1:p.Val316fs
LRG_672t1:c.900_901insCGACACATCAGCCCTCAAGCCAAAGCTCTCCTTCAGGATAAGGACGA
LRG_672:g.14541_14542insACGACACATCAGCCCTCAAGCCAAAGCTCTCCTTCAGGATAAGGACG
LRG_672p1:p.Val316Aspfs
NC_000023.10:g.100653456_100653457insTCGTCCTTATCCTGAAGGAGAGCTTTGGCTTGAGGGCTGATGTGTCG
NM_000169.2:c.900_901insCGACACATCAGCCCTCAAGCCAAAGCTCTCCTTCAGGATAAGGACGA
NR_164783.1:n.1025_1026insACGACACATCAGCCCTCAAGCCAAAGCTCTCCTTCAGGATAAGGACG
NR_176252.1:n.876_877insACGACACATCAGCCCTCAAGCCAAAGCTCTCCTTCAGGATAAGGACG
NR_176253.1:n.1083_1084insACGACACATCAGCCCTCAAGCCAAAGCTCTCCTTCAGGATAAGGACG

Protein change:

V316fs

Links:

dbSNP: rs2147471979

NCBI 1000 Genomes Browser:

rs2147471979

Molecular consequence:

NM_000169.3:c.946_947insACGACACATCAGCCCTCAAGCCAAAGCTCTCCTTCAGGATAAGGACG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406747.1:c.1069_1070insACGACACATCAGCCCTCAAGCCAAAGCTCTCCTTCAGGATAAGGACG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406748.1:c.946_947insACGACACATCAGCCCTCAAGCCAAAGCTCTCCTTCAGGATAAGGACG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001199973.2:c.300+3011_300+3012insTCGTCCTTATCCTGAAGGAGAGCTTTGGCTTGAGGGCTGATGTGTCG - intron variant - [Sequence Ontology: SO:0001627]
NM_001199974.2:c.177+6646_177+6647insTCGTCCTTATCCTGAAGGAGAGCTTTGGCTTGAGGGCTGATGTGTCG - intron variant - [Sequence Ontology: SO:0001627]
NR_164783.1:n.1025_1026insACGACACATCAGCCCTCAAGCCAAAGCTCTCCTTCAGGATAAGGACG - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176252.1:n.876_877insACGACACATCAGCCCTCAAGCCAAAGCTCTCCTTCAGGATAAGGACG - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176253.1:n.1083_1084insACGACACATCAGCCCTCAAGCCAAAGCTCTCCTTCAGGATAAGGACG - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

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

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cytochrome oxidase subunit 1, partial (mitochondrion) [Camptogramma scripturata]
cytochrome oxidase subunit 1, partial (mitochondrion) [Camptogramma scripturata]
gi|2698112379|gb|WXB32695.1|

Protein
Mief1 mitochondrial elongation factor 1 [Mus musculus]
Mief1 mitochondrial elongation factor 1 [Mus musculus]
Gene ID:239555

Gene
239555[uid] AND (alive[prop]) (1)
Gene
AGENCOURT_8216370 NICHD_XGC_Emb4 Xenopus laevis cDNA clone IMAGE:4683659 5', mRN...
AGENCOURT_8216370 NICHD_XGC_Emb4 Xenopus laevis cDNA clone IMAGE:4683659 5', mRNA sequence
gi|21872447|gnl|dbEST|12885261|gb|B 50.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001994759	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 28, 2021)	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

SCV001994759

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Oct 28, 2021)

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	yes	1	not provided	not provided	1	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 3billion, SCV001994759.1

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

Description

Frameshift: predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. It is not observed in the gnomAD v2.1.1 dataset. This variant is shared with the affected son. Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

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

Last Updated: Sep 16, 2024

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