ABCA2 ATP binding cassette subfamily A member 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ABCA2provided by HGNC
Official Full Name: ATP binding cassette subfamily A member 2provided by HGNC
Primary source: HGNC:HGNC:32
See related: Ensembl:ENSG00000107331 MIM:600047; AllianceGenome:HGNC:32
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: ABC2; IDPOGSA
Summary: The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intracellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the ABC1 subfamily. Members of the ABC1 subfamily comprise the only major ABC subfamily found exclusively in multicellular eukaryotes. This protein is highly expressed in brain tissue and may play a role in macrophage lipid metabolism and neural development. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression: Broad expression in brain (RPKM 47.6), thyroid (RPKM 9.5) and 20 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 9q34.3

Exon count:: 50

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (137007234..137028922, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (149241651..149263357, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (139901686..139923374, complement)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Novel compound heterozygous ABCA2 variants cause IDPOGSA, a variable phenotypic syndrome with intellectual disability.
Title: Novel compound heterozygous ABCA2 variants cause IDPOGSA, a variable phenotypic syndrome with intellectual disability.
A polymorphism in ABCA2 is associated with neutropenia induced by capecitabine in Japanese patients with colorectal cancer.
Title: A polymorphism in ABCA2 is associated with neutropenia induced by capecitabine in Japanese patients with colorectal cancer.
Role of ABCA2 and its single nucleotide polymorphisms (4873T>A and 4879G>C) in the regulation of multi-drug resistance in oral squamous carcinoma cells.
Title: Role of ABCA2 and its single nucleotide polymorphisms (4873T>A and 4879G>C) in the regulation of multi-drug resistance in oral squamous carcinoma cells.
Results from a Genome-Wide Association Study (GWAS) in Mastocytosis Reveal New Gene Polymorphisms Associated with WHO Subgroups.
Title: Results from a Genome-Wide Association Study (GWAS) in Mastocytosis Reveal New Gene Polymorphisms Associated with WHO Subgroups.
High expression of ABCA2 is associated with drug resistance in pediatric acute lymphoblastic leukemia.
Title: MicroRNA-326 and microRNA-200c: Two novel biomarkers for diagnosis and prognosis of pediatric acute lymphoblastic leukemia.
The analyses results suggested ABCA2 mRNA expression was upregulated significantly in AD compared with controls in all datasets.
Title: ATP Binding Cassette Subfamily A Member 2 (ABCA2) Expression and Methylation are Associated with Alzheimer's Disease.
Our findings indicate a considerable and direct relationship between mRNA expression levels of ABCA2, ABCA3, MDR1, and MRP1 genes and positive minimal residual disease (MRD) measured after one year of treatment.
Title: mRNA expression profile of multidrug-resistant genes in acute lymphoblastic leukemia of children, a prognostic value for ABCA3 and ABCA2.
Down-regulation of the ATP-binding cassette transporter 2 (Abca2) reduces amyloid-beta production by altering Nicastrin maturation and intracellular localization.
Title: Down-regulation of the ATP-binding cassette transporter 2 (Abca2) reduces amyloid-β production by altering Nicastrin maturation and intracellular localization.
SLC2A1/GLUT1, SLC1A3/EAAT1, and SLC1A2/EAAT2 were the main SLC proteins whereas ABCG2/BCRP, ABCB1/MDR1, ABCA2 and ABCA8 were the main ABC quantified in isolated brain microvessels
Title: Transcriptomic and quantitative proteomic analysis of transporters and drug metabolizing enzymes in freshly isolated human brain microvessels.
A possible biochemical mechanism links ABCA2 expression, amyloid precursor protein processing, and Alzheimer's disease.
Title: The ATP-binding cassette transporter-2 (ABCA2) increases endogenous amyloid precursor protein expression and Aβ fragment generation.

Submit: New GeneRIF Correction See all GeneRIFs (21)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Intellectual developmental disorder with poor growth and with or without seizures or ataxia MedGen: C5394135 OMIM: 618808 GeneReviews: Not available	not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-X78031 (e-PCR)
- UniSTS:55552

D11S949E (e-PCR)
- UniSTS:147460

RH71205 (e-PCR)
- UniSTS:66879

RH101989 (e-PCR)
- UniSTS:96323

NoName (e-PCR)
- UniSTS:481875

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ABC-type transporter activity	IEA Inferred from Electronic Annotation more info
enables ATP binding	IDA Inferred from Direct Assay more info	PubMed
enables ATP binding	ISS Inferred from Sequence or Structural Similarity more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables ATPase-coupled transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables ATPase-coupled transmembrane transporter activity	NAS Non-traceable Author Statement more info	PubMed
enables ceramide floppase activity	IDA Inferred from Direct Assay more info	PubMed
enables endopeptidase regulator activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables lipid transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables nucleotide binding	NAS Non-traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within central nervous system myelin formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in central nervous system myelin formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in cholesterol homeostasis	IEP Inferred from Expression Pattern more info	PubMed
involved_in ganglioside metabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in glycosphingolipid metabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in intracellular sphingolipid homeostasis	IDA Inferred from Direct Assay more info	PubMed
involved_in lipid metabolic process	NAS Non-traceable Author Statement more info	PubMed
involved_in lipid transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in locomotory behavior	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of negative regulation of cholesterol efflux	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of negative regulation of intracellular cholesterol transport	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of negative regulation of low-density lipoprotein receptor activity	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of negative regulation of receptor-mediated endocytosis involved in cholesterol transport	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of negative regulation of steroid metabolic process	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in positive regulation of amyloid precursor protein biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of positive regulation of amyloid precursor protein catabolic process	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of positive regulation of amyloid precursor protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of positive regulation of amyloid-beta formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of amyloid-beta formation	ISS Inferred from Sequence or Structural Similarity more info	PubMed
acts_upstream_of positive regulation of low-density lipoprotein particle receptor catabolic process	IDA Inferred from Direct Assay more info	PubMed
NOT involved_in regulation of cholesterol biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of intracellular cholesterol transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of intracellular cholesterol transport	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of regulation of post-translational protein modification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of protein glycosylation	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in regulation of protein localization to cell periphery	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in regulation of protein localization to cell surface	ISS Inferred from Sequence or Structural Similarity more info	PubMed
acts_upstream_of regulation of steroid metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in response to cholesterol	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to steroid hormone	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to xenobiotic stimulus	TAS Traceable Author Statement more info	PubMed
involved_in sphingomyelin metabolic process	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_positive_effect sphingosine biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in transmembrane transport	NAS Non-traceable Author Statement more info	PubMed
involved_in transport across blood-brain barrier	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
part_of ATP-binding cassette (ABC) transporter complex	NAS Non-traceable Author Statement more info	PubMed
located_in cytoplasmic vesicle	ISS Inferred from Sequence or Structural Similarity more info
located_in endosome	IDA Inferred from Direct Assay more info	PubMed
located_in endosome membrane	IEA Inferred from Electronic Annotation more info
is_active_in intracellular membrane-bounded organelle	IBA Inferred from Biological aspect of Ancestor more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in lysosomal membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in lysosomal membrane	NAS Non-traceable Author Statement more info	PubMed
located_in lysosome	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	HDA more info	PubMed
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	NAS Non-traceable Author Statement more info	PubMed
located_in microtubule organizing center	ISS Inferred from Sequence or Structural Similarity more info
is_active_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: ATP-binding cassette sub-family A member 2

Names: ATP-binding cassette 2; ATP-binding cassette transporter 2; ATP-binding cassette, sub-family A (ABC1), member 2; ATP-binding cassette, sub-family A, member 2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_011789.1 RefSeqGene

Range

5686..26689

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001411042.1 → NP_001397971.1 ATP-binding cassette sub-family A member 2 isoform c

Status: REVIEWED

Source sequence(s)

AL807752, KF458947

Consensus CDS

CCDS94538.1

UniProtKB/Swiss-Prot

A6NED5, Q5SPY5, Q5W9G5, Q76MW7, Q9BZC7, Q9HC28

Related

ENSP00000360666.3, ENST00000371605.7
NM_001606.5 → NP_001597.2 ATP-binding cassette sub-family A member 2 isoform a

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the predominant isoform (a).

Source sequence(s)

AF178941, AL525193, AL807752, BC029282, BE273611, BF516223, BM474929, BM921499, CD676110, DB168116

Consensus CDS

CCDS43909.1

UniProtKB/TrEMBL

A0A087WXK5

Related

ENSP00000344155.6, ENST00000341511.11

Conserved Domains (2) summary

TIGR01257
Location:1 → 2368

rim_protein; retinal-specific rim ABC transporter

cd03263
Location:2051 → 2274

ABC_subfamily_A; ATP-binding cassette domain of the lipid transporters, subfamily A
NM_212533.3 → NP_997698.1 ATP-binding cassette sub-family A member 2 isoform b

See identical proteins and their annotated locations for NP_997698.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and coding region compared to variant 1. The resulting isoform (b) is longer and has a distinct N-terminus compared to isoform a.

Source sequence(s)

AF178941, AL525193, AL807752, BC029282, BE273611, BF516223, BM474929, BM921499, DB168116

Consensus CDS

CCDS94539.1

UniProtKB/TrEMBL

A0A087WXK5

Related

ENSP00000481105.2, ENST00000614293.5

Conserved Domains (2) summary

TIGR01257
Location:58 → 2398

rim_protein; retinal-specific rim ABC transporter

cd03263
Location:2081 → 2304

ABC_subfamily_A; ATP-binding cassette domain of the lipid transporters, subfamily A