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Aliases for ABCA13 Gene

Aliases for ABCA13 Gene

  • ATP Binding Cassette Subfamily A Member 13 2 3 5
  • ATP-Binding Cassette, Sub-Family A (ABC1), Member 13 2 3
  • ATP-Binding Cassette Sub-Family A Member 13 Variant 2 3
  • ATP-Binding Cassette Sub-Family A Member 13 Variant 3 3
  • ATP-Binding Cassette Sub-Family A Member 13 3
  • ATP Binding Cassette Transporter A13 3

External Ids for ABCA13 Gene

Previous GeneCards Identifiers for ABCA13 Gene

  • GC07P048023
  • GC07P047982
  • GC07P048015

Summaries for ABCA13 Gene

Entrez Gene Summary for ABCA13 Gene

  • In human, the ATP-binding cassette (ABC) family of transmembrane transporters has at least 48 genes and 7 gene subfamilies. This gene is a member of ABC gene subfamily A (ABCA). Genes within the ABCA family typically encode several thousand amino acids. Like other ABC transmembrane transporter proteins, this protein has 12 or more transmembrane alpha-helix domains that likely arrange to form a single central chamber with multiple substrate binding sites. It is also predicted to have two large extracellular domains and two nucleotide binding domains as is typical for ABCA proteins. Alternative splice variants have been described but their biological validity has not been demonstrated.[provided by RefSeq, Mar 2009]

GeneCards Summary for ABCA13 Gene

ABCA13 (ATP Binding Cassette Subfamily A Member 13) is a Protein Coding gene. Diseases associated with ABCA13 include Shwachman-Diamond Syndrome 1 and Schizophrenia. Among its related pathways are CDK-mediated phosphorylation and removal of Cdc6 and Innate Immune System. Gene Ontology (GO) annotations related to this gene include ATPase activity and cholesterol transporter activity. An important paralog of this gene is ABCA12.

Gene Wiki entry for ABCA13 Gene

Additional gene information for ABCA13 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ABCA13 Gene

Genomics for ABCA13 Gene

GeneHancer (GH) Regulatory Elements for ABCA13 Gene

Promoters and enhancers for ABCA13 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
GH07J048171 Promoter 0.5 EPDnew 650.7 0.0 -9 0.1 ABCA13 LOC105375271
GH07J048081 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 9.8 -80.4 -80397 18.7 FOXA2 SMAD1 ARNT ARID4B SIN3A FEZF1 IRF4 YY1 POLR2B E2F8 UPP1 HUS1 ENSG00000225507 PKD1L1 SUN3 ABCA13 LOC105375271
GH07J048109 Enhancer 1.3 Ensembl ENCODE dbSUPER 10.8 -61.5 -61491 1.6 ELF3 FOXA2 RB1 ARID4B SIN3A IRF4 ZNF48 RAD21 RARA YY1 UPP1 C7orf57 PKD1L1 HUS1 ABCA13 LOC105375271
GH07J048200 Enhancer 0.5 ENCODE 25.9 +29.8 29772 0.8 SOX6 IKZF1 NFE2 EMSY ABCA13 UPP1 GC07M048357
GH07J048255 Enhancer 0.8 FANTOM5 ENCODE 10.7 +83.8 83795 0.3 JUNB MEF2B BATF ATF2 BCL11A CREB1 ATF7 CREM RUNX3 MAFK ABCA13 UPP1 HUS1 GC07M048357
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ABCA13 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ABCA13 gene promoter:
  • LUN-1
  • Nkx6-1
  • AML1a
  • POU2F1
  • POU2F1a
  • POU2F1b
  • POU2F1c
  • SRF (504 AA)
  • SRF
  • HSF1short

Genomic Locations for ABCA13 Gene

Genomic Locations for ABCA13 Gene
476,050 bases
Plus strand
476,038 bases
Plus strand

Genomic View for ABCA13 Gene

Genes around ABCA13 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ABCA13 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ABCA13 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ABCA13 Gene

Proteins for ABCA13 Gene

  • Protein details for ABCA13 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    ATP-binding cassette sub-family A member 13
    Protein Accession:
    Secondary Accessions:
    • K9LC76
    • K9LC79
    • K9LCX7
    • K9LDK8
    • K9LDY4
    • Q6ZTT7
    • Q86WI2
    • Q8N248

    Protein attributes for ABCA13 Gene

    5058 amino acids
    Molecular mass:
    576159 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAC03623.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAC86492.1; Type=Erroneous termination; Positions=123; Note=Translated as Glu.; Evidence={ECO:0000305}; Sequence=BAC86492.1; Type=Frameshift; Positions=156; Evidence={ECO:0000305};

    Alternative splice isoforms for ABCA13 Gene

neXtProt entry for ABCA13 Gene

Post-translational modifications for ABCA13 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for ABCA13 Gene

Domains & Families for ABCA13 Gene

Gene Families for ABCA13 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for ABCA13 Gene

Suggested Antigen Peptide Sequences for ABCA13 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the ABC transporter superfamily.
  • Belongs to the ABC transporter superfamily.
genes like me logo Genes that share domains with ABCA13: view

Function for ABCA13 Gene

Phenotypes From GWAS Catalog for ABCA13 Gene

Gene Ontology (GO) - Molecular Function for ABCA13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005524 ATP binding IEA --
GO:0016887 ATPase activity IEA --
GO:0042626 ATPase activity, coupled to transmembrane movement of substances IBA,IEA --
genes like me logo Genes that share ontologies with ABCA13: view
genes like me logo Genes that share phenotypes with ABCA13: view

Animal Models for ABCA13 Gene

MGI Knock Outs for ABCA13:
  • Abca13 Abca13<tm1b(EUCOMM)Wtsi>

Animal Model Products

  • Taconic Biosciences Mouse Models for ABCA13

miRNA for ABCA13 Gene

miRTarBase miRNAs that target ABCA13

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for ABCA13 Gene

Localization for ABCA13 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ABCA13 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 ABCA13 gene
Compartment Confidence
plasma membrane 5
lysosome 4
golgi apparatus 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for ABCA13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030667 secretory granule membrane TAS --
GO:0035577 azurophil granule membrane TAS --
genes like me logo Genes that share ontologies with ABCA13: view

Pathways & Interactions for ABCA13 Gene

genes like me logo Genes that share pathways with ABCA13: view

Pathways by source for ABCA13 Gene

3 Reactome pathways for ABCA13 Gene
1 KEGG pathway for ABCA13 Gene

Gene Ontology (GO) - Biological Process for ABCA13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006869 lipid transport IBA --
GO:0043312 neutrophil degranulation TAS --
GO:0055085 transmembrane transport IEA --
genes like me logo Genes that share ontologies with ABCA13: view

No data available for SIGNOR curated interactions for ABCA13 Gene

Drugs & Compounds for ABCA13 Gene

No Compound Related Data Available

Transcripts for ABCA13 Gene

Unigene Clusters for ABCA13 Gene

ATP-binding cassette, sub-family A (ABC1), member 13:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ABCA13 Gene

No ASD Table

Relevant External Links for ABCA13 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ABCA13 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ABCA13 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for ABCA13 Gene

This gene is overexpressed in Whole Blood (x12.5), Thyroid (x8.6), and Esophagus - Mucosa (x4.8).

Protein differential expression in normal tissues from HIPED for ABCA13 Gene

This gene is overexpressed in Nasal epithelium (59.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for ABCA13 Gene

Protein tissue co-expression partners for ABCA13 Gene

NURSA nuclear receptor signaling pathways regulating expression of ABCA13 Gene:


SOURCE GeneReport for Unigene cluster for ABCA13 Gene:


mRNA Expression by UniProt/SwissProt for ABCA13 Gene:

Tissue specificity: Significantly expressed in the bone marrow, trachea, testis, thyroid and lung as well as in skin fibroblasts.

Evidence on tissue expression from TISSUES for ABCA13 Gene

  • Lung(4.1)
genes like me logo Genes that share expression patterns with ABCA13: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for ABCA13 Gene

Orthologs for ABCA13 Gene

This gene was present in the common ancestor of animals.

Orthologs for ABCA13 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ABCA13 34 33
  • 99.03 (n)
(Bos Taurus)
Mammalia ABCA13 34 33
  • 77.18 (n)
(Mus musculus)
Mammalia Abca13 16 34 33
  • 76.24 (n)
(Rattus norvegicus)
Mammalia Abca13 33
  • 75.53 (n)
(Canis familiaris)
Mammalia ABCA13 34 33
  • 75.22 (n)
(Monodelphis domestica)
Mammalia ABCA13 34
  • 57 (a)
(Danio rerio)
Actinopterygii abch1 34
  • 18 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG34120 34
  • 22 (a)
(Caenorhabditis elegans)
Secernentea abt-2 34
  • 24 (a)
Species where no ortholog for ABCA13 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • chicken (Gallus gallus)
  • 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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for ABCA13 Gene

Gene Tree for ABCA13 (if available)
Gene Tree for ABCA13 (if available)
Evolutionary constrained regions (ECRs) for ABCA13: view image

Paralogs for ABCA13 Gene

Paralogs for ABCA13 Gene

(17) SIMAP similar genes for ABCA13 Gene using alignment to 11 proteins:

  • F5H7B7_HUMAN
  • H0Y4D2_HUMAN
  • H7C0U5_HUMAN
  • K9LC76_HUMAN
  • K9LC79_HUMAN
  • L8E9N5_HUMAN
genes like me logo Genes that share paralogs with ABCA13: view

Variants for ABCA13 Gene

Sequence variations from dbSNP and Humsavar for ABCA13 Gene

SNP ID Clin Chr 07 pos Variation AA Info Type
rs797045205 likely-pathogenic, Schizophrenia 48,387,961(+) T/C genic_downstream_transcript_variant, intron_variant, splice_donor_variant
rs781126037 pathogenic, not provided 48,273,998(+) AAAAAAA/AAAAAA/AAAAAAAA coding_sequence_variant, frameshift, non_coding_transcript_variant
rs530287474 uncertain-significance, not specified 48,587,265(+) G/A coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs544438554 uncertain-significance, not specified 48,403,729(+) C/T coding_sequence_variant, genic_downstream_transcript_variant, non_coding_transcript_variant, stop_gained
rs559926336 uncertain-significance, not specified 48,244,615(+) C/A/T coding_sequence_variant, missense_variant, non_coding_transcript_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for ABCA13 Gene

Variant ID Type Subtype PubMed ID
dgv1910e212 CNV loss 25503493
dgv1911e212 CNV loss 25503493
dgv6346n100 CNV loss 25217958
esv1790237 CNV insertion 17803354
esv21443 CNV loss 19812545
esv2314060 CNV deletion 18987734
esv2421774 CNV deletion 20811451
esv2600887 CNV deletion 19546169
esv2623647 CNV loss 19546169
esv2659311 CNV deletion 23128226
esv2662109 CNV deletion 23128226
esv2671369 CNV deletion 23128226
esv2672976 CNV deletion 23128226
esv2734370 CNV deletion 23290073
esv275242 CNV gain+loss 21479260
esv2761325 CNV loss 21179565
esv2764056 CNV loss 21179565
esv3541602 CNV deletion 23714750
esv3541603 CNV deletion 23714750
esv3571843 CNV loss 25503493
esv3571846 CNV loss 25503493
esv3613079 CNV loss 21293372
esv3613081 CNV loss 21293372
esv3613082 CNV loss 21293372
esv3613083 CNV loss 21293372
esv3613084 CNV gain 21293372
esv3613085 CNV gain 21293372
esv3613086 CNV loss 21293372
esv3613087 CNV loss 21293372
esv3613088 CNV loss 21293372
esv3613089 CNV loss 21293372
esv3613090 CNV loss 21293372
esv3891106 CNV loss 25118596
esv993578 CNV gain 20482838
nsv1027414 CNV loss 25217958
nsv1032135 CNV loss 25217958
nsv1114934 CNV deletion 24896259
nsv1128315 CNV deletion 24896259
nsv1161520 CNV deletion 26073780
nsv442041 CNV loss 18776908
nsv442042 CNV loss 18776908
nsv464442 CNV gain 19166990
nsv470221 CNV gain 18288195
nsv472040 CNV novel sequence insertion 20440878
nsv472900 CNV novel sequence insertion 20440878
nsv478665 CNV novel sequence insertion 20440878
nsv479338 CNV novel sequence insertion 20440878
nsv479725 CNV novel sequence insertion 20440878
nsv499496 CNV loss 21111241
nsv514415 CNV gain 21397061
nsv514416 CNV loss 21397061
nsv521082 CNV loss 19592680
nsv524173 CNV loss 19592680
nsv527625 CNV loss 19592680
nsv528154 CNV loss 19592680
nsv5733 CNV deletion 18451855
nsv606893 CNV gain 21841781
nsv606894 CNV loss 21841781
nsv830992 CNV gain 17160897

Variation tolerance for ABCA13 Gene

Residual Variation Intolerance Score: 99.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 17.23; 98.11% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ABCA13 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ABCA13 Gene

Disorders for ABCA13 Gene

MalaCards: The human disease database

(2) MalaCards diseases for ABCA13 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
shwachman-diamond syndrome 1
  • sds1
  • sczd
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for ABCA13

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 ABCA13: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ABCA13 Gene

Publications for ABCA13 Gene

  1. The human ATP binding cassette gene ABCA13, located on chromosome 7p12.3, encodes a 5058 amino acid protein with an extracellular domain encoded in part by a 4.8-kb conserved exon. (PMID: 12697998) Prades C … Dean M (Cytogenetic and genome research 2002) 2 3 4 58
  2. Evidence for an alternative genomic structure, mRNA and protein sequence of human ABCA13. (PMID: 23266639) Maeß MB … Lorkowski S (Gene 2013) 3 4 58
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  4. A common variant in DRD3 receptor is associated with autism spectrum disorder. (PMID: 19058789) de Krom M … van Ree JM (Biological psychiatry 2009) 3 44 58
  5. A cytogenetic abnormality and rare coding variants identify ABCA13 as a candidate gene in schizophrenia, bipolar disorder, and depression. (PMID: 19944402) Knight HM … Blackwood DH (American journal of human genetics 2009) 3 44 58

Products for ABCA13 Gene

Sources for ABCA13 Gene

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