NM_001371904.1(APOA5):c.990_993del (p.Asp332fs) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Dec 19, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001256823.4

Allele description [Variation Report for NM_001371904.1(APOA5):c.990_993del (p.Asp332fs)]

NM_001371904.1(APOA5):c.990_993del (p.Asp332fs)

Gene:

APOA5:apolipoprotein A5 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

11q23.3

Genomic location:

Preferred name:

NM_001371904.1(APOA5):c.990_993del (p.Asp332fs)

HGVS:

NC_000011.10:g.116790236TGTT[1]
NG_015894.2:g.7178AACA[1]
NM_001166598.2:c.990_993del
NM_001371904.1:c.990_993delMANE SELECT
NM_052968.5:c.990_993del
NP_001160070.1:p.Asp332fs
NP_001358833.1:p.Asp332fs
NP_443200.2:p.Asp332fs
NC_000011.10:g.116790236_116790239delTGTT
NC_000011.9:g.116660952TGTT[1]
NC_000011.9:g.116660952_116660955del
NG_015894.1:g.7178AACA[1]
NM_052968.4:c.990_993delAACA

Protein change:

D332fs

Links:

dbSNP: rs774150500

NCBI 1000 Genomes Browser:

rs774150500

Molecular consequence:

NM_001166598.2:c.990_993del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001371904.1:c.990_993del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_052968.5:c.990_993del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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PREDICTED: Actinidia eriantha ABC transporter G family member 9-like (LOC1307896...
PREDICTED: Actinidia eriantha ABC transporter G family member 9-like (LOC130789625), transcript variant X2, mRNA
gi|2526878336|ref|XM_057650431.1|

Nucleotide
PREDICTED: Actinidia eriantha ABC transporter G family member 9-like (LOC1307896...
PREDICTED: Actinidia eriantha ABC transporter G family member 9-like (LOC130789625), transcript variant X3, mRNA
gi|2526878338|ref|XM_057650432.1|

Nucleotide
Saccharomyces cerevisiae YJM456 chromosome XVI sequence
Saccharomyces cerevisiae YJM456 chromosome XVI sequence
gi|1034676781|gb|CP006224.2|

Nucleotide
Lemur catta isolate:mLemCat1
Lemur catta isolate:mLemCat1
Lemur catta (Ring-tailed lemur) genome, mLemCat1, primary haplotype

BioProject
optimal (72)
Conserved Domains

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001433290	Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 21, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004294940	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 19, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 24591733, 29748148, 30420299, 23307945, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001433290

Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jan 21, 2020)

germline

clinical testing

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

SCV004294940

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 19, 2023)

germline

clinical testing

PubMed (5)
[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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
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

Clinical features and genetic analysis of three patients with severe hypertriglyceridaemia.

Hooper AJ, Kurtkoti J, Hamilton-Craig I, Burnett JR.

Ann Clin Biochem. 2014 Jul;51(Pt 4):485-9. doi: 10.1177/0004563214525767. Epub 2014 Mar 3.

PubMed [citation]

PMID:: 24591733

See all PubMed Citations (6)

Details of each submission

From Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute, SCV001433290.1

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

#	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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004294940.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This sequence change creates a premature translational stop signal (p.Asp332Valfs*5) in the APOA5 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 35 amino acid(s) of the APOA5 protein. This variant is present in population databases (rs774150500, gnomAD 0.006%). This premature translational stop signal has been observed in individual(s) with APOA5-related conditions (PMID: 23307945, 24591733, 29748148, 30420299; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as p.Q330Q fs X6. ClinVar contains an entry for this variant (Variation ID: 978324). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this premature translational stop signal affects APOA5 function (PMID: 23307945). For these reasons, this variant has been classified as Pathogenic.

#	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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