NM_005502.4(ABCA1):c.1857_1858delinsAT (p.Met619_Gln620delinsIleTer) AND Hypoalphalipoproteinemia, primary, 1

Germline classification:: Likely pathogenic (1 submission)
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:: RCV003482190.1

Allele description [Variation Report for NM_005502.4(ABCA1):c.1857_1858delinsAT (p.Met619_Gln620delinsIleTer)]

NM_005502.4(ABCA1):c.1857_1858delinsAT (p.Met619_Gln620delinsIleTer)

Gene:

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

Variant type:

Indel

Cytogenetic location:

9q31.1

Genomic location:

Preferred name:

NM_005502.4(ABCA1):c.1857_1858delinsAT (p.Met619_Gln620delinsIleTer)

HGVS:

NC_000009.12:g.104830959_104830960delinsAT
NG_007981.1:g.102196_102197delinsAT
NM_005502.4:c.1857_1858delinsATMANE SELECT
NP_005493.2:p.Met619_Gln620delinsIleTer
LRG_542t1:c.1857_1858delinsAT
LRG_542:g.102196_102197delinsAT
LRG_542p1:p.Met619_Gln620delinsIleTer
NC_000009.11:g.107593240_107593241delinsAT

Molecular consequence:

NM_005502.4:c.1857_1858delinsAT - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

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

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004227981	Department Of Human Genetics, Institute Of Clinical And Translational Research, Biomedical Research Center, Slovak Academy Of Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	germline	research	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004227981

Department Of Human Genetics, Institute Of Clinical And Translational Research, Biomedical Research Center, Slovak Academy Of Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic

germline

research

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	3	1	not provided	not provided	yes	research

Citations

PubMed

APOC3 and ABCA1 variants in unusual combined hypolipidaemia showing premature peripheral vascular disease.

Pos Z, Khedr M, Radvanszky J, Penesova A, Hekel R, Szemes T, Ranganath LR, Zatkova A.

Bratisl Lek Listy. 2023;124(5):351-355. doi: 10.4149/BLL_2023_053.

PubMed [citation]

PMID:: 36876364

Details of each submission

From Department Of Human Genetics, Institute Of Clinical And Translational Research, Biomedical Research Center, Slovak Academy Of Sciences, SCV004227981.1

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

Description

This variant was found in a 57-years-old male patient with combined hypolipidaemia who presented with premature peripheral vascular disease. His two sons, 32- and 27-years-old, who manifested a tendency to low lipid levels were also analyzed by WES analysis, based on which we could exclude the major effect of the variants within the genes most frequently mutated in hypolipidaemia (ANGPTL3, SAR1B, APOB, PCSK9, MTTP, LIPC). In all three individuals we identified a novel ABCA1 variant NM_005502.4:c.1857_1858delinsAT, possibly responsible for the decreased HDL levels. The proband and one of his sons also shared the splicing APOC3 variant NM_000040.3:c.55+1G>A (rs138326449), known to be associated with decreased TG levels. We believe that the lipid profile in the probands appears to result from a combination of mainly these two independent pathogenic variants (PMID: 36876364).

#	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		3	not provided	1	not provided

Last Updated: Jun 9, 2024

ClinVar

Relating variation to medicine