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Aliases for ABCA3 Gene

Aliases for ABCA3 Gene

  • ATP Binding Cassette Subfamily A Member 3 2 3 5
  • ATP-Binding Cassette, Sub-Family A (ABC1), Member 3 2 3
  • ATP-Binding Cassette Transporter 3 3 4
  • ABC-C Transporter 3 4
  • ABC3 3 4
  • ATP-Binding Cassette Sub-Family A Member 3 3
  • ATP-Binding Cassette 3 4
  • ABC Transporter 3 3
  • EST111653 3
  • LBM180 3
  • ABC-C 3
  • SMDP3 3

External Ids for ABCA3 Gene

Previous HGNC Symbols for ABCA3 Gene

  • ABC3

Previous GeneCards Identifiers for ABCA3 Gene

  • GC16P002406
  • GC16M002351
  • GC16M002265
  • GC16M002327
  • GC16M002251
  • GC16M002330

Summaries for ABCA3 Gene

Entrez Gene Summary for ABCA3 Gene

  • 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]

GeneCards Summary for ABCA3 Gene

ABCA3 (ATP Binding Cassette Subfamily A Member 3) is a Protein Coding gene. Diseases associated with ABCA3 include Surfactant Metabolism Dysfunction, Pulmonary, 3 and Pulmonary Fibrosis, Idiopathic. Among its related pathways are CDK-mediated phosphorylation and removal of Cdc6 and Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds. Gene Ontology (GO) annotations related to this gene include transporter activity and ATPase activity, coupled to transmembrane movement of substances. An important paralog of this gene is ABCA1.

UniProtKB/Swiss-Prot for ABCA3 Gene

  • Plays an important role in the formation of pulmonary surfactant, probably by transporting lipids such as cholesterol.

Gene Wiki entry for ABCA3 Gene

Additional gene information for ABCA3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ABCA3 Gene

Genomics for ABCA3 Gene

GeneHancer (GH) Regulatory Elements for ABCA3 Gene

Promoters and enhancers for ABCA3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16J002679 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 650.1 -340.8 -340805 4.1 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ENSG00000279901 KCTD5 PIR38297 PIR43814 PIR61225 ABCA3 TBL3 ENSG00000261613 ZNF597 E4F1
GH16J002339 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 650.7 +0.5 477 2.2 CLOCK MLX ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 ABCA17P ABCA3 PIR33563 CRAMP1 UNKL ZNF263 ENSG00000261123 TELO2 ZNF75A TSC2
GH16J002329 Promoter 0.8 EPDnew 650.4 +11.0 11030 0.1 NCOA3 ZNF217 CTBP1 GATA3 ESRRA NFXL1 ABCA3 RPS16P7 PIR38241
GH16J002459 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 11.5 -119.4 -119408 1.5 HDGF PKNOX1 ATF1 MLX ARID4B SIN3A ZNF2 ETS1 ZNF121 POLR2B ENSG00000260874 LOC105371050 TEDC2 SRRM2 ZNF263 ENSG00000255513 SNORA64 LOC105371055 TELO2 ENSG00000260954
GH16J002506 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 11.6 -168.0 -168048 4.4 PKNOX1 SMAD1 RAD21 ZNF143 ATF7 IKZF2 RUNX3 EGR2 SMARCA5 CBFB TBC1D24 PDPK1 CEMP1 ABCA17P ABCA3 CCNF SRRM2 ATP6V0C ENSG00000260272 GC16M002495
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around ABCA3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ABCA3 gene promoter:

Genomic Locations for ABCA3 Gene

Genomic Locations for ABCA3 Gene
64,869 bases
Minus strand

Genomic View for ABCA3 Gene

Genes around ABCA3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ABCA3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ABCA3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ABCA3 Gene

Proteins for ABCA3 Gene

  • Protein details for ABCA3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    ATP-binding cassette sub-family A member 3
    Protein Accession:
    Secondary Accessions:
    • B2RU09
    • Q54A95
    • Q6P5P9
    • Q92473

    Protein attributes for ABCA3 Gene

    1704 amino acids
    Molecular mass:
    191362 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for ABCA3 Gene


neXtProt entry for ABCA3 Gene

Post-translational modifications for ABCA3 Gene

  • Ubiquitination at posLast=16681668
  • Modification sites at PhosphoSitePlus

Other Protein References for ABCA3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for ABCA3 Gene

Domains & Families for ABCA3 Gene

Gene Families for ABCA3 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Potential drug targets
  • Predicted membrane proteins
  • Transporters

Protein Domains for ABCA3 Gene

Suggested Antigen Peptide Sequences for ABCA3 Gene

Graphical View of Domain Structure for InterPro Entry



  • Multifunctional polypeptide with two homologous halves, each containing a hydrophobic membrane-anchoring domain and an ATP binding cassette (ABC) domain.
  • Belongs to the ABC transporter superfamily. ABCA family.
  • Multifunctional polypeptide with two homologous halves, each containing a hydrophobic membrane-anchoring domain and an ATP binding cassette (ABC) domain.
  • Belongs to the ABC transporter superfamily. ABCA family.
genes like me logo Genes that share domains with ABCA3: view

Function for ABCA3 Gene

Molecular function for ABCA3 Gene

UniProtKB/Swiss-Prot Function:
Plays an important role in the formation of pulmonary surfactant, probably by transporting lipids such as cholesterol.
GENATLAS Biochemistry:
ATP binding cassette superfamily,subfamily A,member 3,involved in resistance to xenobiotics,mouse ABC2 (mu ABC2) homolog,highly expressed in lung,brain,heart,pancreas

Phenotypes From GWAS Catalog for ABCA3 Gene

Gene Ontology (GO) - Molecular Function for ABCA3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005215 transporter activity TAS 9027511
GO:0005319 lipid transporter activity TAS --
GO:0005524 ATP binding TAS,IEA --
GO:0016887 ATPase activity IEA --
GO:0042626 ATPase activity, coupled to transmembrane movement of substances IEA,TAS --
genes like me logo Genes that share ontologies with ABCA3: view
genes like me logo Genes that share phenotypes with ABCA3: view

Human Phenotype Ontology for ABCA3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for ABCA3 Gene

MGI Knock Outs for ABCA3:

Animal Model Products

  • Taconic Biosciences Mouse Models for ABCA3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for ABCA3 Gene

Localization for ABCA3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ABCA3 Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ABCA3 gene
Compartment Confidence
plasma membrane 5
extracellular 5
cytoskeleton 2
nucleus 2
cytosol 2
endoplasmic reticulum 1
lysosome 1
golgi apparatus 1
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ABCA3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space HDA 22664934
GO:0005886 plasma membrane IDA 11718719
GO:0016020 membrane TAS 9027511
GO:0016021 integral component of membrane TAS,IEA --
GO:0043231 intracellular membrane-bounded organelle IBA --
genes like me logo Genes that share ontologies with ABCA3: view

Pathways & Interactions for ABCA3 Gene

genes like me logo Genes that share pathways with ABCA3: view

Gene Ontology (GO) - Biological Process for ABCA3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006869 lipid transport IBA --
GO:0042493 response to drug TAS 8706931
GO:0044267 cellular protein metabolic process TAS --
GO:0051384 response to glucocorticoid IEA --
GO:0055085 transmembrane transport TAS --
genes like me logo Genes that share ontologies with ABCA3: view

No data available for SIGNOR curated interactions for ABCA3 Gene

Drugs & Compounds for ABCA3 Gene

(6) Drugs for ABCA3 Gene - From: DrugBank, ClinicalTrials, FDA Approved Drugs, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
imatinib Approved Pharma Transporter, substrate Kinase Inhibitors, SRC/BCR-ABL tyrosine kinase inhibitors 0
Protein C Approved Pharma 126
Gleevec Approved May 2001 Pharma 0
Pulmonary Surfactants Pharma 122
Respiratory System Agents Pharma 5297

(1) Additional Compounds for ABCA3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with ABCA3: view

Transcripts for ABCA3 Gene

mRNA/cDNA for ABCA3 Gene

Unigene Clusters for ABCA3 Gene

ATP-binding cassette, sub-family A (ABC1), member 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ABCA3 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^
SP1: -
SP2: - -

ExUns: 25a · 25b ^ 26 ^ 27a · 27b ^ 28 ^ 29 ^ 30 ^ 31 ^ 32
SP1: -
SP2: -

Relevant External Links for ABCA3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ABCA3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ABCA3 Gene

mRNA differential expression in normal tissues according to GTEx for ABCA3 Gene

This gene is overexpressed in Lung (x8.9).

Protein differential expression in normal tissues from HIPED for ABCA3 Gene

This gene is overexpressed in Lung (43.0), Brain (12.4), and Pancreatic juice (6.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for ABCA3 Gene

NURSA nuclear receptor signaling pathways regulating expression of ABCA3 Gene:


SOURCE GeneReport for Unigene cluster for ABCA3 Gene:


mRNA Expression by UniProt/SwissProt for ABCA3 Gene:

Tissue specificity: Highly expressed in lung, followed by brain, pancreas, skeletal muscle and heart. Weakly expressed in placenta, kidney and liver. Also expressed in medullary thyroid carcinoma cells (MTC) and in C-cell carcinoma.

Evidence on tissue expression from TISSUES for ABCA3 Gene

  • Nervous system(4.8)
  • Lung(4.7)

Phenotype-based relationships between genes and organs from Gene ORGANizer for ABCA3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • immune
  • respiratory
  • skeletal muscle
  • diaphragm
  • lung
  • peripheral nerve
  • peripheral nervous system
genes like me logo Genes that share expression patterns with ABCA3: view

No data available for Protein tissue co-expression partners for ABCA3 Gene

Orthologs for ABCA3 Gene

This gene was present in the common ancestor of animals.

Orthologs for ABCA3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ABCA3 34 33
  • 99.24 (n)
(Bos Taurus)
Mammalia ABCA3 34 33
  • 87.55 (n)
(Canis familiaris)
Mammalia ABCA3 34 33
  • 87.44 (n)
(Rattus norvegicus)
Mammalia Abca3 33
  • 84.6 (n)
(Mus musculus)
Mammalia Abca3 16 34 33
  • 84.49 (n)
(Monodelphis domestica)
Mammalia ABCA3 34
  • 75 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 66 (a)
-- 34
  • 61 (a)
(Gallus gallus)
Aves ABCA3 34 33
  • 73.4 (n)
(Anolis carolinensis)
Reptilia -- 34
  • 79 (a)
-- 34
  • 65 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia abca3 33
  • 64.44 (n)
Str.16690 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.5193 33
(Danio rerio)
Actinopterygii abca3b 34 33
  • 66.89 (n)
ABCA3 (2 of 2) 34
  • 55 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.5550 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006379 33
  • 52.03 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG1718 34 35 33
  • 51.08 (n)
CG6052 34 35
  • 32 (a)
BG:DS00797.5 35
  • 31 (a)
CG1819 35
  • 26 (a)
CG1494 35
  • 25 (a)
CG8908 35
  • 25 (a)
CG1801 35
  • 22 (a)
(Caenorhabditis elegans)
Secernentea abt-4 33
  • 48.17 (n)
abt-6 34
  • 45 (a)
ced-7 35
  • 26 (a)
Species where no ortholog for ABCA3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for ABCA3 Gene

Gene Tree for ABCA3 (if available)
Gene Tree for ABCA3 (if available)
Evolutionary constrained regions (ECRs) for ABCA3: view image

Paralogs for ABCA3 Gene

Paralogs for ABCA3 Gene

(12) SIMAP similar genes for ABCA3 Gene using alignment to 4 proteins:

  • H0Y3H2_HUMAN
  • Q6P5P9_HUMAN Pseudogenes for ABCA3 Gene

genes like me logo Genes that share paralogs with ABCA3: view

Variants for ABCA3 Gene

Sequence variations from dbSNP and Humsavar for ABCA3 Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs1001542091 uncertain-significance, Pulmonary Surfactant Metabolism Dysfunction, Recessive 2,299,541(-) A/G intron_variant
rs114420154 uncertain-significance, Pulmonary Surfactant Metabolism Dysfunction, Recessive 2,281,235(-) A/G intron_variant
rs117031141 benign, likely-benign, not specified, Pulmonary Surfactant Metabolism Dysfunction, Recessive 2,324,393(-) G/A/T intron_variant
rs117515055 likely-benign, Pulmonary Surfactant Metabolism Dysfunction, Recessive 2,326,116(-) G/A coding_sequence_variant, synonymous_variant
rs117603931 likely-benign, not specified, not provided 2,319,591(-) C/T coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for ABCA3 Gene

Variant ID Type Subtype PubMed ID
esv2422427 CNV duplication 17116639
esv2675164 CNV deletion 23128226
esv2750379 CNV deletion 23290073
esv2750380 CNV deletion 23290073
esv2750381 CNV deletion 23290073
esv2750382 CNV deletion 23290073
esv2750383 CNV deletion 23290073
esv3553009 CNV deletion 23714750
esv4221 CNV loss 18987735
esv6856 CNV loss 19470904
nsv1052260 CNV gain 25217958
nsv1115888 CNV deletion 24896259
nsv1131103 CNV deletion 24896259
nsv1140053 CNV deletion 24896259
nsv1150821 CNV deletion 26484159
nsv457353 CNV loss 19166990
nsv471072 CNV loss 18288195
nsv571201 CNV loss 21841781
nsv571202 CNV loss 21841781
nsv827512 CNV gain 20364138
nsv952902 CNV deletion 24416366
nsv984251 CNV duplication 23825009

Variation tolerance for ABCA3 Gene

Residual Variation Intolerance Score: 6.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.98; 49.63% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ABCA3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ABCA3 Gene

Disorders for ABCA3 Gene

MalaCards: The human disease database

(10) MalaCards diseases for ABCA3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search ABCA3 in MalaCards View complete list of genes associated with diseases


  • Pulmonary surfactant metabolism dysfunction 3 (SMDP3) [MIM:610921]: A rare lung disorder due to impaired surfactant homeostasis. It is characterized by alveolar filling with floccular material that stains positive using the periodic acid-Schiff method and is derived from surfactant phospholipids and protein components. Excessive lipoproteins accumulation in the alveoli results in severe respiratory distress. {ECO:0000269 PubMed:15044640}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for ABCA3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with ABCA3: view

No data available for Genatlas for ABCA3 Gene

Publications for ABCA3 Gene

  1. Primary structure of a novel ABC transporter with a chromosomal localization on the band encoding the multidrug resistance-associated protein. (PMID: 8706931) Klugbauer N … Hofmann F (FEBS letters 1996) 2 3 4 22 58
  2. Population and disease-based prevalence of the common mutations associated with surfactant deficiency. (PMID: 18317237) Garmany TH … Hamvas A (Pediatric research 2008) 3 22 44 58
  3. ABCA3 gene mutations in newborns with fatal surfactant deficiency. (PMID: 15044640) Shulenin S … Dean M (The New England journal of medicine 2004) 3 4 44 58
  4. ABCA3 is a lamellar body membrane protein in human lung alveolar type II cells. (PMID: 11718719) Yamano G … Inagaki N (FEBS letters 2001) 3 4 22 58
  5. The cloning of a human ABC gene (ABC3) mapping to chromosome 16p13.3. (PMID: 9027511) Connors TD … Burn TC (Genomics 1997) 3 4 22 58

Products for ABCA3 Gene

Sources for ABCA3 Gene

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