ABCA4 ATP binding cassette subfamily A member 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ABCA4provided by HGNC
Official Full Name: ATP binding cassette subfamily A member 4provided by HGNC
Primary source: HGNC:HGNC:34
See related: Ensembl:ENSG00000198691 MIM:601691; AllianceGenome:HGNC:34
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: FFM; RMP; ABCR; RP19; STGD; ABC10; ARMD2; CORD3; STGD1
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 a retina-specific ABC transporter with N-retinylidene-PE as a substrate. It is expressed exclusively in retina photoreceptor cells, and the gene product mediates transport of an essental molecule, all-trans-retinal aldehyde (atRAL), across the photoreceptor cell membrane. Mutations in this gene are found in patients diagnosed with Stargardt disease, a form of juvenile-onset macular degeneration. Mutations in this gene are also associated with retinitis pigmentosa-19, cone-rod dystrophy type 3, early-onset severe retinal dystrophy, fundus flavimaculatus, and macular degeneration age-related 2. [provided by RefSeq, Sep 2019]
Expression: Biased expression in kidney (RPKM 2.3), small intestine (RPKM 0.8) and 6 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p22.1

Exon count:: 50

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (93992834..94121148, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (93841050..93969344, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (94458390..94586704, complement)

Chromosome 1 - NC_000001.11 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 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?

Virus-like particles as robust tools for functional assessment: Deciphering the pathogenicity of ABCA4 genetic variants of uncertain significance.
Title: Virus-like particles as robust tools for functional assessment: Deciphering the pathogenicity of ABCA4 genetic variants of uncertain significance.
Structural and functional characterization of the nucleotide-binding domains of ABCA4 and their role in Stargardt disease.
Title: Structural and functional characterization of the nucleotide-binding domains of ABCA4 and their role in Stargardt disease.
Genotypic spectrum of ABCA4-associated retinal degenerations in 211 unrelated Mexican patients: identification of 22 novel disease-causing variants.
Title: Genotypic spectrum of ABCA4-associated retinal degenerations in 211 unrelated Mexican patients: identification of 22 novel disease-causing variants.
Novel and Recurrent Copy Number Variants in ABCA4-Associated Retinopathy.
Title: Novel and Recurrent Copy Number Variants in ABCA4-Associated Retinopathy.
GENETIC FACTORS AND CHARACTERISTICS ON SPECTRAL-DOMAIN OPTICAL COHERENCE TOMOGRAPHY ARE ASSOCIATED WITH CHOROIDAL THICKNESS IN ABCA4 -RELATED RETINOPATHY.
Title: GENETIC FACTORS AND CHARACTERISTICS ON SPECTRAL-DOMAIN OPTICAL COHERENCE TOMOGRAPHY ARE ASSOCIATED WITH CHOROIDAL THICKNESS IN ABCA4 -RELATED RETINOPATHY.
Understanding and Rescuing the Splicing Defect Caused by the Frequent ABCA4 Variant c.4253+43G>A Underlying Stargardt Disease.
Title: Understanding and Rescuing the Splicing Defect Caused by the Frequent ABCA4 Variant c.4253+43G>A Underlying Stargardt Disease.
Protein modeling and in silico analysis to assess pathogenicity of ABCA4 variants in patients with inherited retinal disease.
Title: Protein modeling and in silico analysis to assess pathogenicity of ABCA4 variants in patients with inherited retinal disease.
Major Contribution of c.[1622T>C;3113C>T] Complex Allele and c.5882G>A Variant in ABCA4-Related Retinal Dystrophy in an Eastern European Population.
Title: Major Contribution of c.[1622T>C;3113C>T] Complex Allele and c.5882G>A Variant in ABCA4-Related Retinal Dystrophy in an Eastern European Population.
Stargardt disease-associated missense and synonymous ABCA4 variants result in aberrant splicing.
Title: Stargardt disease-associated missense and synonymous ABCA4 variants result in aberrant splicing.
Comprehensive genetic analysis reveals the mutational landscape of ABCA4-associated retinal dystrophy in a Chinese cohort.
Title: Comprehensive genetic analysis reveals the mutational landscape of ABCA4-associated retinal dystrophy in a Chinese cohort.

Submit: New GeneRIF Correction See all GeneRIFs (267)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Age related macular degeneration 2 MedGen: C3495438 OMIM: 153800 GeneReviews: Not available	not available
Cone-rod dystrophy 3 MedGen: C1858806 OMIM: 604116 GeneReviews: Not available	not available
Retinitis pigmentosa 19 MedGen: C1866422 OMIM: 601718 GeneReviews: Nonsyndromic Retinitis Pigmentosa Overview	not available
Severe early-childhood-onset retinal dystrophy MedGen: C1855465 OMIM: 248200 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
Genetic predictors of fibrin D-dimer levels in healthy adults. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association scan for survival on dialysis in African-Americans with type 2 diabetes. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies novel loci associated with concentrations of four plasma phospholipid fatty acids in the de novo lipogenesis pathway: results from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortiu EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analyses of nonsyndromic cleft lip with or without cleft palate identify six new risk loci. 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

AL009647 (e-PCR)
- UniSTS:6215

SHGC-31446 (e-PCR)
- UniSTS:6474

SHGC-83480 (e-PCR)
- UniSTS:101963

ABCA4_2633 (e-PCR)
- UniSTS:280415

SHGC-31244 (e-PCR)
- UniSTS:57967

SHGC-82674 (e-PCR)
- UniSTS:95630

SHGC-31368 (e-PCR)
- UniSTS:66474

RH119981 (e-PCR)
- UniSTS:133305

SHGC-132421 (e-PCR)
- UniSTS:181945

WI-22788 (e-PCR)
- UniSTS:64973

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 11-cis retinal binding	IDA Inferred from Direct Assay more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
enables ATP hydrolysis activity	ISS Inferred from Sequence or Structural Similarity more info
enables ATPase-coupled intramembrane lipid transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables ATPase-coupled transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables GTPase activity	ISS Inferred from Sequence or Structural Similarity more info
enables N-retinylidene-phosphatidylethanolamine flippase activity	ISS Inferred from Sequence or Structural Similarity more info
enables all-trans retinal binding	IDA Inferred from Direct Assay more info	PubMed
enables flippase activity	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylethanolamine flippase activity	IDA Inferred from Direct Assay more info	PubMed
enables phospholipid transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables retinoid binding	ISS Inferred from Sequence or Structural Similarity more info
enables retinol transmembrane transporter activity	TAS Traceable Author Statement more info

Process	Evidence Code	Pubs
involved_in lipid transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in phospholipid transfer to membrane	IEA Inferred from Electronic Annotation more info
involved_in phospholipid translocation	IDA Inferred from Direct Assay more info	PubMed
involved_in photoreceptor cell maintenance	IEA Inferred from Electronic Annotation more info
involved_in phototransduction, visible light	TAS Traceable Author Statement more info	PubMed
involved_in retinal metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in retinal metabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in retinoid metabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in retinoid metabolic process	TAS Traceable Author Statement more info
involved_in retinol transport	IEA Inferred from Electronic Annotation more info
involved_in transmembrane transport	TAS Traceable Author Statement more info
involved_in visual perception	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoplasmic vesicle	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
is_active_in intracellular membrane-bounded organelle	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	TAS Traceable Author Statement more info	PubMed
located_in photoreceptor disc membrane	TAS Traceable Author Statement more info
located_in photoreceptor outer segment	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in rod photoreceptor disc membrane	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: retinal-specific phospholipid-transporting ATPase ABCA4

Names: ATP binding cassette transporter; ATP-binding cassette sub-family A member 4; ATP-binding cassette transporter, retinal-specific; ATP-binding cassette, sub-family A (ABC1), member 4; ATP-binding transporter, retina-specific; RIM ABC transporter; RIM protein; RIM proteinv; photoreceptor rim protein; retina-specific ABC transporter; retinal-specific ATP-binding cassette transporter; stargardt disease protein

NP_000341.2

EC 7.6.2.1

NP_001412253.1

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_009073.2 RefSeqGene

Range

5000..133314

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000350.3 → NP_000341.2 retinal-specific phospholipid-transporting ATPase ABCA4 isoform 1

See identical proteins and their annotated locations for NP_000341.2

Status: REVIEWED

Source sequence(s)

AC093579, AC105278

Consensus CDS

CCDS747.1

UniProtKB/Swiss-Prot

O15112, O60438, O60915, P78363, Q0QD48, Q4LE31

Related

ENSP00000359245.3, ENST00000370225.4

Conserved Domains (1) summary

TIGR01257
Location:1 → 2272

rim_protein; retinal-specific rim ABC transporter
NM_001425324.1 → NP_001412253.1 retinal-specific phospholipid-transporting ATPase ABCA4 isoform 2

Status: REVIEWED

Source sequence(s)

AC093579, AC105278