NM_000039.3(APOA1):c.178T>G (p.Ser60Ala) AND Hypoalphalipoproteinemia, primary, 1

Germline classification:: Benign (1 submission)
Last evaluated:: Apr 27, 2017
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:: RCV001106514.4

Allele description [Variation Report for NM_000039.3(APOA1):c.178T>G (p.Ser60Ala)]

NM_000039.3(APOA1):c.178T>G (p.Ser60Ala)

Genes:

APOA1-AS:APOA1 antisense RNA [Gene - OMIM - HGNC]
APOA1:apolipoprotein A1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q23.3

Genomic location:

Preferred name:

NM_000039.3(APOA1):c.178T>G (p.Ser60Ala)

HGVS:

NC_000011.10:g.116837023A>C
NG_012021.1:g.5600T>G
NM_000039.3:c.178T>GMANE SELECT
NM_001318017.2:c.178T>G
NM_001318018.2:c.178T>G
NM_001318021.2:c.-150T>G
NP_000030.1:p.Ser60Ala
NP_000030.1:p.Ser60Ala
NP_001304946.1:p.Ser60Ala
NP_001304947.1:p.Ser60Ala
LRG_767t1:c.178T>G
LRG_767:g.5600T>G
LRG_767p1:p.Ser60Ala
NC_000011.9:g.116707739A>C
NC_000011.9:g.116707739A>C
NM_000039.1:c.178T>G
NM_001318021.1:c.-150T>G

Protein change:

S60A

Links:

dbSNP: rs199759119

NCBI 1000 Genomes Browser:

rs199759119

Molecular consequence:

NM_000039.3:c.178T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001318017.2:c.178T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001318018.2:c.178T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hypoalphalipoproteinemia, primary, 1
Identifiers:: MONDO: MONDO:0011393; MedGen: C5231558; Orphanet: 425; OMIM: 604091

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001263587	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Apr 27, 2017)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 17303779, 21820994, 20884842, 23770607, 23209431 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001263587

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Benign
(Apr 27, 2017)

germline

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

Citation Link

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

Genetic etiology of isolated low HDL syndrome: incidence and heterogeneity of efflux defects.

Kiss RS, Kavaslar N, Okuhira K, Freeman MW, Walter S, Milne RW, McPherson R, Marcel YL.

Arterioscler Thromb Vasc Biol. 2007 May;27(5):1139-45. Epub 2007 Feb 15.

PubMed [citation]

PMID:: 17303779

Amyloidogenicity and clinical phenotype associated with five novel mutations in apolipoprotein A-I.

Rowczenio D, Dogan A, Theis JD, Vrana JA, Lachmann HJ, Wechalekar AD, Gilbertson JA, Hunt T, Gibbs SD, Sattianayagam PT, Pinney JH, Hawkins PN, Gillmore JD.

Am J Pathol. 2011 Oct;179(4):1978-87. doi: 10.1016/j.ajpath.2011.06.024. Epub 2011 Aug 5.

PubMed [citation]

PMID:: 21820994
PMCID:: PMC3181365

See all PubMed Citations (5)

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001263587.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.

#	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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