ABCA7 ATP binding cassette subfamily A member 7 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ABCA7provided by HGNC
Official Full Name: ATP binding cassette subfamily A member 7provided by HGNC
Primary source: HGNC:HGNC:37
See related: Ensembl:ENSG00000064687 MIM:605414; AllianceGenome:HGNC:37
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: AD9; ABCX; ABCA-SSN
Summary: The 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 intra-cellular 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 full transporter has been detected predominantly in myelo-lymphatic tissues with the highest expression in peripheral leukocytes, thymus, spleen, and bone marrow. The function of this protein is not yet known; however, the expression pattern suggests a role in lipid homeostasis in cells of the immune system. [provided by RefSeq, Jul 2008]
Expression: Broad expression in bone marrow (RPKM 11.7), spleen (RPKM 9.6) and 22 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19p13.3

Exon count:: 48

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (1040107..1065572)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (1002776..1030237)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (1040106..1065571)

Chromosome 19 - NC_000019.10 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?

CSF biomarker analysis of ABCA7 mutation carriers suggests altered APP processing and reduced inflammatory response.
Title: CSF biomarker analysis of ABCA7 mutation carriers suggests altered APP processing and reduced inflammatory response.
Down-Regulation of ABCA7 in Human Microglia, Astrocyte and THP-1 Cell Lines by Cholesterol Depletion, IL-1beta and TNFalpha, or PMA.
Title: Down-Regulation of ABCA7 in Human Microglia, Astrocyte and THP-1 Cell Lines by Cholesterol Depletion, IL-1β and TNFα, or PMA.
ABCA7-Associated Clinical Features and Molecular Mechanisms in Alzheimer's Disease.
Title: ABCA7-Associated Clinical Features and Molecular Mechanisms in Alzheimer's Disease.
High-Quality Sleep Mitigates ABCA7-Related Generalization Deficits in Healthy Older African Americans.
Title: High-Quality Sleep Mitigates ABCA7-Related Generalization Deficits in Healthy Older African Americans.
Aberrant DNA Methylation, Expression, and Occurrence of Transcript Variants of the ABC Transporter ABCA7 in Breast Cancer.
Title: Aberrant DNA Methylation, Expression, and Occurrence of Transcript Variants of the ABC Transporter ABCA7 in Breast Cancer.
Cryo-EM structures of human ABCA7 provide insights into its phospholipid translocation mechanisms.
Title: Cryo-EM structures of human ABCA7 provide insights into its phospholipid translocation mechanisms.
SNP-by-CpG Site Interactions in ABCA7 Are Associated with Cognition in Older African Americans.
Title: SNP-by-CpG Site Interactions in ABCA7 Are Associated with Cognition in Older African Americans.
ATP-binding cassette protein ABCA7 deficiency impairs sphingomyelin synthesis, cognitive discrimination, and synaptic plasticity in the entorhinal cortex.
Title: ATP-binding cassette protein ABCA7 deficiency impairs sphingomyelin synthesis, cognitive discrimination, and synaptic plasticity in the entorhinal cortex.
Association between ABCA7 gene polymorphisms and Parkinson's disease susceptibility in a northern Chinese Han population.
Title: Association between ABCA7 gene polymorphisms and Parkinson's disease susceptibility in a northern Chinese Han population.
ABCA7, a Genetic Risk Factor Associated with Alzheimer's Disease Risk in African Americans.
Title: ABCA7, a Genetic Risk Factor Associated with Alzheimer's Disease Risk in African Americans.

Submit: New GeneRIF Correction See all GeneRIFs (66)

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
Alzheimer disease 9 MedGen: C4282179 OMIM: 608907 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Variants in the ATP-binding cassette transporter (ABCA7), apolipoprotein E &#x000cf;&#x000b5;4,and the risk of late-onset Alzheimer disease in African Americans. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

RH70510 (e-PCR)
- UniSTS:10876

CNN2_8268 (e-PCR)
- UniSTS:467613

D1S3693 (e-PCR)
- UniSTS:474271

ABCA7_2692 (e-PCR)
- UniSTS:462003

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ABC-type transporter activity	IEA Inferred from Electronic Annotation more info
enables ATP binding	IEA Inferred from Electronic Annotation 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 apolipoprotein A-I receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables apolipoprotein A-I receptor activity	IDA Inferred from Direct Assay more info	PubMed
enables floppase activity	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylcholine floppase activity	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylcholine floppase activity	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylserine floppase activity	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylserine floppase activity	IDA Inferred from Direct Assay more info	PubMed
enables phospholipid transporter activity	IGI Inferred from Genetic Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in amyloid-beta clearance by cellular catabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in amyloid-beta formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in apolipoprotein A-I-mediated signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in cholesterol efflux	IBA Inferred from Biological aspect of Ancestor more info
involved_in cholesterol efflux	IDA Inferred from Direct Assay more info	PubMed
involved_in high-density lipoprotein particle assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in memory	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of MAPK cascade	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of PERK-mediated unfolded protein response	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of amyloid precursor protein biosynthetic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of amyloid-beta formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of endocytosis	ISS Inferred from Sequence or Structural Similarity more info
involved_in peptide cross-linking	ISS Inferred from Sequence or Structural Similarity more info
involved_in phagocytosis	IEA Inferred from Electronic Annotation more info
involved_in phospholipid efflux	IBA Inferred from Biological aspect of Ancestor more info
involved_in phospholipid efflux	IDA Inferred from Direct Assay more info	PubMed
involved_in phospholipid efflux	IGI Inferred from Genetic Interaction more info	PubMed
involved_in phospholipid translocation	IDA Inferred from Direct Assay more info	PubMed
involved_in plasma membrane raft organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of ERK1 and ERK2 cascade	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of amyloid-beta clearance	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cholesterol efflux	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of engulfment of apoptotic cell	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of phagocytosis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of phospholipid efflux	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of protein localization to cell surface	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein localization to nucleus	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of amyloid precursor protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of lipid metabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in visual learning	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info
located_in Golgi membrane	IEA Inferred from Electronic Annotation more info
located_in cell junction	IDA Inferred from Direct Assay more info
located_in cell surface	ISS Inferred from Sequence or Structural Similarity more info
located_in early endosome membrane	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum	IEA Inferred from Electronic Annotation more info
located_in glial cell projection	ISS Inferred from Sequence or Structural Similarity more info
is_active_in intracellular membrane-bounded organelle	IBA Inferred from Biological aspect of Ancestor more info
located_in phagocytic cup	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
located_in ruffle membrane	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: phospholipid-transporting ATPase ABCA7

Names: ATP-binding cassette sub-family A member 7; ATP-binding cassette, sub-family A (ABC1), member 7; autoantigen SS-N; macrophage ABC transporter

NP_061985.2

EC 7.6.2.1

XP_006722679.1

EC 7.6.2.1

XP_006722680.1

EC 7.6.2.1

XP_011525935.1

EC 7.6.2.1

XP_011525936.1

EC 7.6.2.1

XP_011525937.1

EC 7.6.2.1

XP_047294000.1

EC 7.6.2.1

XP_047294001.1

EC 7.6.2.1

XP_047294002.1

EC 7.6.2.1

XP_047294003.1

EC 7.6.2.1

XP_047294004.1

EC 7.6.2.1

XP_047294005.1

EC 7.6.2.1

XP_047294007.1

EC 7.6.2.1

XP_047294008.1

EC 7.6.2.1

XP_047294009.1

EC 7.6.2.1

XP_047294010.1

EC 7.6.2.1

XP_047294011.1

EC 7.6.2.1

XP_047294012.1

EC 7.6.2.1

XP_054175491.1

EC 7.6.2.1

XP_054175492.1

EC 7.6.2.1

XP_054175493.1

EC 7.6.2.1

XP_054175494.1

EC 7.6.2.1

XP_054175495.1

EC 7.6.2.1

XP_054175496.1

EC 7.6.2.1

XP_054175497.1

EC 7.6.2.1

XP_054175498.1

EC 7.6.2.1

XP_054175499.1

EC 7.6.2.1

XP_054175500.1

EC 7.6.2.1

XP_054175501.1

EC 7.6.2.1

XP_054175502.1

EC 7.6.2.1

XP_054175503.1

EC 7.6.2.1

XP_054175504.1

EC 7.6.2.1

XP_054175505.1

EC 7.6.2.1

XP_054175506.1

EC 7.6.2.1

XP_054175507.1

EC 7.6.2.1

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_046909.1 RefSeqGene

Range

5005..30470

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_019112.4 → NP_061985.2 phospholipid-transporting ATPase ABCA7

See identical proteins and their annotated locations for NP_061985.2

Status: REVIEWED

Source sequence(s)

AF250238, AF328787, AK097344, BU675136, CD629701, DC405492

Consensus CDS

CCDS12055.1

UniProtKB/Swiss-Prot

Q8IZY2, Q96S58, Q9BZC4, Q9NR73, Q9UKP8

Related

ENSP00000263094.6, ENST00000263094.11

Conserved Domains (1) summary

TIGR01257
Location:1 → 2109

rim_protein; retinal-specific rim ABC transporter

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

1040107..1065572

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006722616.2 → XP_006722679.1 phospholipid-transporting ATPase ABCA7 isoform X3

Conserved Domains (1) summary

TIGR01257
Location:1 → 2091

rim_protein; retinal-specific rim ABC transporter
XM_047438047.1 → XP_047294003.1 phospholipid-transporting ATPase ABCA7 isoform X4
XM_047438048.1 → XP_047294004.1 phospholipid-transporting ATPase ABCA7 isoform X5
XM_047438045.1 → XP_047294001.1 phospholipid-transporting ATPase ABCA7 isoform X2
XM_047438044.1 → XP_047294000.1 phospholipid-transporting ATPase ABCA7 isoform X1

UniProtKB/Swiss-Prot

Q8IZY2, Q96S58, Q9BZC4, Q9NR73, Q9UKP8
XM_047438046.1 → XP_047294002.1 phospholipid-transporting ATPase ABCA7 isoform X3
XM_047438051.1 → XP_047294007.1 phospholipid-transporting ATPase ABCA7 isoform X7
XM_047438052.1 → XP_047294008.1 phospholipid-transporting ATPase ABCA7 isoform X8
XM_047438053.1 → XP_047294009.1 phospholipid-transporting ATPase ABCA7 isoform X11
XM_011527633.3 → XP_011525935.1 phospholipid-transporting ATPase ABCA7 isoform X10

Conserved Domains (1) summary

TIGR01257
Location:1 → 1610

rim_protein; retinal-specific rim ABC transporter
XM_006722617.3 → XP_006722680.1 phospholipid-transporting ATPase ABCA7 isoform X9

Conserved Domains (1) summary

TIGR01257
Location:1 → 1610

rim_protein; retinal-specific rim ABC transporter
XM_011527635.2 → XP_011525937.1 phospholipid-transporting ATPase ABCA7 isoform X12

See identical proteins and their annotated locations for XP_011525937.1

Conserved Domains (1) summary

TIGR01257
Location:1 → 1472

rim_protein; retinal-specific rim ABC transporter
XM_011527634.2 → XP_011525936.1 phospholipid-transporting ATPase ABCA7 isoform X12

See identical proteins and their annotated locations for XP_011525936.1

Conserved Domains (1) summary

TIGR01257
Location:1 → 1472

rim_protein; retinal-specific rim ABC transporter
XM_047438056.1 → XP_047294012.1 phospholipid-transporting ATPase ABCA7 isoform X14
XM_047438049.1 → XP_047294005.1 phospholipid-transporting ATPase ABCA7 isoform X6
XM_047438055.1 → XP_047294011.1 phospholipid-transporting ATPase ABCA7 isoform X13
XM_047438054.1 → XP_047294010.1 phospholipid-transporting ATPase ABCA7 isoform X13

RNA

XR_936149.2 RNA Sequence
XR_936152.2 RNA Sequence
XR_007066538.1 RNA Sequence
XR_936154.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060943.1 Alternate T2T-CHM13v2.0

Range

1002776..1030237

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054319518.1 → XP_054175493.1 phospholipid-transporting ATPase ABCA7 isoform X3
XM_054319520.1 → XP_054175495.1 phospholipid-transporting ATPase ABCA7 isoform X4
XM_054319521.1 → XP_054175496.1 phospholipid-transporting ATPase ABCA7 isoform X5
XM_054319517.1 → XP_054175492.1 phospholipid-transporting ATPase ABCA7 isoform X2
XM_054319516.1 → XP_054175491.1 phospholipid-transporting ATPase ABCA7 isoform X1
XM_054319519.1 → XP_054175494.1 phospholipid-transporting ATPase ABCA7 isoform X3
XM_054319523.1 → XP_054175498.1 phospholipid-transporting ATPase ABCA7 isoform X7
XM_054319524.1 → XP_054175499.1 phospholipid-transporting ATPase ABCA7 isoform X8
XM_054319527.1 → XP_054175502.1 phospholipid-transporting ATPase ABCA7 isoform X11
XM_054319526.1 → XP_054175501.1 phospholipid-transporting ATPase ABCA7 isoform X10
XM_054319525.1 → XP_054175500.1 phospholipid-transporting ATPase ABCA7 isoform X9
XM_054319529.1 → XP_054175504.1 phospholipid-transporting ATPase ABCA7 isoform X12
XM_054319528.1 → XP_054175503.1 phospholipid-transporting ATPase ABCA7 isoform X12
XM_054319532.1 → XP_054175507.1 phospholipid-transporting ATPase ABCA7 isoform X14
XM_054319522.1 → XP_054175497.1 phospholipid-transporting ATPase ABCA7 isoform X6
XM_054319531.1 → XP_054175506.1 phospholipid-transporting ATPase ABCA7 isoform X13
XM_054319530.1 → XP_054175505.1 phospholipid-transporting ATPase ABCA7 isoform X13

RNA

XR_008485063.1 RNA Sequence
XR_008485065.1 RNA Sequence
XR_008485064.1 RNA Sequence
XR_008485066.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_033308.1: Suppressed sequence

Description

NM_033308.1: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the N-terminus of the protein.