NM_005502.4(ABCA1):c.254C>T (p.Pro85Leu) AND Hypoalphalipoproteinemia, primary, 1

Germline classification:: Likely 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:: RCV000346255.6

Allele description [Variation Report for NM_005502.4(ABCA1):c.254C>T (p.Pro85Leu)]

NM_005502.4(ABCA1):c.254C>T (p.Pro85Leu)

Gene:

ABCA1:ATP binding cassette subfamily A member 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q31.1

Genomic location:

Preferred name:

NM_005502.4(ABCA1):c.254C>T (p.Pro85Leu)

HGVS:

NC_000009.12:g.104884475G>A
NG_007981.1:g.48681C>T
NM_005502.4:c.254C>TMANE SELECT
NP_005493.2:p.Pro85Leu
LRG_542t1:c.254C>T
LRG_542:g.48681C>T
LRG_542p1:p.Pro85Leu
NC_000009.11:g.107646756G>A
NM_005502.3:c.254C>T
O95477:p.Pro85Leu

Protein change:

P85L

Links:

UniProtKB: O95477#VAR_017529; dbSNP: rs145183203

NCBI 1000 Genomes Browser:

rs145183203

Molecular consequence:

NM_005502.4:c.254C>T - 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
SCV000476366	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Apr 27, 2017)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 23770607, 12204794, 12763760, 15297675 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000476366

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Apr 27, 2017)

germline

clinical testing

PubMed (4)
[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

Whole-genome sequence-based analysis of high-density lipoprotein cholesterol.

Morrison AC, Voorman A, Johnson AD, Liu X, Yu J, Li A, Muzny D, Yu F, Rice K, Zhu C, Bis J, Heiss G, O'Donnell CJ, Psaty BM, Cupples LA, Gibbs R, Boerwinkle E; Cohorts for Heart and Aging Research in Genetic Epidemiology (CHARGE) Consortium..

Nat Genet. 2013 Aug;45(8):899-901. doi: 10.1038/ng.2671. Epub 2013 Jun 16.

PubMed [citation]

PMID:: 23770607
PMCID:: PMC4030301

ABCA1(Alabama): a novel variant associated with HDL deficiency and premature coronary artery disease.

Hong SH, Rhyne J, Zeller K, Miller M.

Atherosclerosis. 2002 Oct;164(2):245-50. Review.

PubMed [citation]

PMID:: 12204794

See all PubMed Citations (4)

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000476366.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

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 determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely 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: Oct 8, 2024

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