ABCA3 ATP binding cassette subfamily A member 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ABCA3provided by HGNC
Official Full Name: ATP binding cassette subfamily A member 3provided by HGNC
Primary source: HGNC:HGNC:33
See related: Ensembl:ENSG00000167972 MIM:601615; AllianceGenome:HGNC:33
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: ABC3; ABC-C; SMDP3; LBM180; EST111653
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. The full transporter encoded by this gene may be involved in development of resistance to xenobiotics and engulfment during programmed cell death. [provided by RefSeq, Jul 2008]
Expression: Biased expression in lung (RPKM 66.7), brain (RPKM 21.3) and 5 other tissues See more
Orthologs: all
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Genomic context

Location:: 16p13.3

Exon count:: 33

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (2275881..2340728, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (2298327..2363113, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (2325882..2390729, complement)

Chromosome 16 - NC_000016.10 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 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?

Evaluation of the Copy Number Variants and Single-Nucleotide Polymorphisms of ABCA3 in Newborns with Respiratory Distress Syndrome-A Pilot Study.
Title: Evaluation of the Copy Number Variants and Single-Nucleotide Polymorphisms of ABCA3 in Newborns with Respiratory Distress Syndrome-A Pilot Study.
Similarities and differences of interstitial lung disease associated with pathogenic variants in SFTPC and ABCA3 in adults.
Title: Similarities and differences of interstitial lung disease associated with pathogenic variants in SFTPC and ABCA3 in adults.
Human pluripotent stem cell modeling of alveolar type 2 cell dysfunction caused by ABCA3 mutations.
Title: Human pluripotent stem cell modeling of alveolar type 2 cell dysfunction caused by ABCA3 mutations.
Interstitial lung disease in a family with bi-allelic variants in ABCA3: non-specific interstitial pneumonitis pattern of injury.
Title: Interstitial lung disease in a family with bi-allelic variants in ABCA3: non-specific interstitial pneumonitis pattern of injury.
Increased Expression of the ABCA1 and ABCA3 Transporter Genes is Associated with Cisplatin Resistance in Breast Cancer Cells.
Title: Increased Expression of the ABCA1 and ABCA3 Transporter Genes is Associated with Cisplatin Resistance in Breast Cancer Cells.
ABCA3 Deficiency-Variant-Specific Response to Hydroxychloroquine.
Title: ABCA3 Deficiency-Variant-Specific Response to Hydroxychloroquine.
ABCA3-related interstitial lung disease beyond infancy.
Title: ABCA3-related interstitial lung disease beyond infancy.
Inherited pulmonary surfactant metabolism disorders in Argentina: Differences between patients with SFTPC and ABCA3 variants.
Title: Inherited pulmonary surfactant metabolism disorders in Argentina: Differences between patients with SFTPC and ABCA3 variants.
Verification of immunology-related genetic associations in BPD supports ABCA3 and five other genes.
Title: Verification of immunology-related genetic associations in BPD supports ABCA3 and five other genes.
Biologic characterization of ABCA3 variants in lung tissue from infants and children with ABCA3 deficiency.
Title: Biologic characterization of ABCA3 variants in lung tissue from infants and children with ABCA3 deficiency.

Submit: New GeneRIF Correction See all GeneRIFs (95)

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
Interstitial lung disease due to ABCA3 deficiency MedGen: C1970456 OMIM: 610921 GeneReviews: Not available	Compare labs

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

D16S662 (e-PCR)
- UniSTS:148791

D16S664 (e-PCR)
- UniSTS:148794

SHGC-61174 (e-PCR)
- UniSTS:83514

D1S3690 (e-PCR)
- UniSTS:474268

D16S291 (e-PCR)
- UniSTS:47526

ABCA3_193 (e-PCR)
- UniSTS:276944

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ABC-type xenobiotic transporter activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IDA Inferred from Direct Assay more info	PubMed
enables ATPase-coupled transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables lipid transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables lipid transporter activity	TAS Traceable Author Statement more info
enables phosphatidylcholine flippase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables phosphatidylcholine transfer activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in intermembrane lipid transfer	IEA Inferred from Electronic Annotation more info
involved_in lipid translocation	IEA Inferred from Electronic Annotation more info
involved_in lipid transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in lipid transport	TAS Traceable Author Statement more info
involved_in lung development	ISS Inferred from Sequence or Structural Similarity more info
involved_in organelle assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in phosphatidylcholine metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in phosphatidylcholine metabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in phosphatidylglycerol metabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in phospholipid homeostasis	IEA Inferred from Electronic Annotation more info
involved_in phospholipid transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cholesterol efflux	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of phospholipid efflux	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of phospholipid transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein homooligomerization	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of lipid biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in regulation of phosphatidylcholine metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to glucocorticoid	IEA Inferred from Electronic Annotation more info
involved_in response to xenobiotic stimulus	TAS Traceable Author Statement more info	PubMed
involved_in surfactant homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in xenobiotic export from cell	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in xenobiotic transmembrane transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in xenobiotic transport	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in alveolar lamellar body	IDA Inferred from Direct Assay more info	PubMed
located_in alveolar lamellar body membrane	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasmic vesicle membrane	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular space	HDA more info	PubMed
is_active_in intracellular membrane-bounded organelle	IBA Inferred from Biological aspect of Ancestor more info
located_in lamellar body	IDA Inferred from Direct Assay more info	PubMed
located_in lamellar body membrane	IDA Inferred from Direct Assay more info	PubMed
located_in lamellar body membrane	TAS Traceable Author Statement more info
located_in late endosome	IDA Inferred from Direct Assay more info	PubMed
located_in lysosomal membrane	IEA Inferred from Electronic Annotation more info
located_in multivesicular body membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: phospholipid-transporting ATPase ABCA3

Names: ABC transporter 3; ABC-C transporter; ATP-binding cassette sub-family A member 3; ATP-binding cassette transporter 3; ATP-binding cassette, sub-family A (ABC1), member 3; xenobiotic-transporting ATPase ABCA3

NP_001080.2

EC 7.6.2.1

EC 7.6.2.2

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_011790.2 RefSeqGene

Range

5000..69847

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001089.3 → NP_001080.2 phospholipid-transporting ATPase ABCA3

See identical proteins and their annotated locations for NP_001080.2

Status: REVIEWED

Source sequence(s)

AC009065, AC098805, AC106820

Consensus CDS

CCDS10466.1

UniProtKB/Swiss-Prot

B2RU09, Q54A95, Q6P5P9, Q92473, Q99758

UniProtKB/TrEMBL

A7MBM9

Related

ENSP00000301732.5, ENST00000301732.10

Conserved Domains (4) summary

TIGR01188
Location:1397 → 1692

drrA; daunorubicin resistance ABC transporter ATP-binding subunit

cd03263
Location:530 → 751

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

COG1131
Location:530 → 839

CcmA; ABC-type multidrug transport system, ATPase component [Defense mechanisms]

pfam12698
Location:923 → 1261

ABC2_membrane_3; ABC-2 family transporter protein