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ACAP3 ArfGAP with coiled-coil, ankyrin repeat and PH domains 3 [ Homo sapiens (human) ]

Gene ID: 116983, updated on 5-Mar-2024

Summary

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Official Symbol
ACAP3provided by HGNC
Official Full Name
ArfGAP with coiled-coil, ankyrin repeat and PH domains 3provided by HGNC
Primary source
HGNC:HGNC:16754
See related
Ensembl:ENSG00000131584 AllianceGenome:HGNC:16754
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CENTB5
Summary
Predicted to enable GTPase activator activity and metal ion binding activity. Predicted to be involved in regulation of catalytic activity. Predicted to act upstream of or within neuron migration and regulation of neuron projection development. Predicted to be located in growth cone. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in skin (RPKM 16.2), brain (RPKM 12.8) and 24 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
1p36.33
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (1292391..1307930, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (723917..739479, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (1227771..1243310, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ubiquitin conjugating enzyme E2 J2 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:1199775-1200974 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1207366-1207874 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1207875-1208381 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1208382-1208889 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 49 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 50 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1210080-1210718 Neighboring gene long intergenic non-protein coding RNA 1786 Neighboring gene MPRA-validated peak7 silencer Neighboring gene sodium channel epithelial 1 subunit delta Neighboring gene CEB15 minisatellite repeat instability region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1223369-1223916 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1223917-1224463 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1224736-1225308 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 51 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1227773-1228318 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1232563-1233499 Neighboring gene microRNA 6726 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1237151-1237752 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1237753-1238352 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1238353-1238953 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1238954-1239553 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1239554-1240154 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 52 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 53 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 54 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 55 Neighboring gene small nucleolar RNA, C/D box 167 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 56 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 57 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 58 Neighboring gene pseudouridine synthase like 1 Neighboring gene microRNA 6727 Neighboring gene integrator complex subunit 11

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Length Polymorphism and Methylation Status of UPS29 Minisatellite of the ACAP3 Gene as Molecular Biomarker of Epilepsy. Sex Differences in Seizure Types and Symptoms. Suchkova IO, et al. Int J Mol Sci, 2020 Dec 2. PMID 33276684, Free PMC Article
  2. [CENTB5 gene expression in human and mouse]. Shubina DM, et al. Mol Biol (Mosk), 2009 May-Jun. PMID 19548526
  3. ACAP3, the GTPase-activating protein specific to the small GTPase Arf6, regulates neuronal migration in the developing cerebral cortex. Miura Y, et al. Biochem Biophys Res Commun, 2017 Nov 18. PMID 28919417
  4. ACAP3 regulates neurite outgrowth through its GAP activity specific to Arf6 in mouse hippocampal neurons. Miura Y, et al. Biochem J, 2016 Sep 1. PMID 27330119
  5. Prediction of the coding sequences of unidentified human genes. XIX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. Nagase T, et al. DNA Res, 2000 Dec 31. PMID 11214970

See all (17) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Length Polymorphism and Methylation Status of UPS29 Minisatellite of the ACAP3 Gene as Molecular Biomarker of Epilepsy. Sex Differences in Seizure Types and Symptoms.
    Title: Length Polymorphism and Methylation Status of UPS29 Minisatellite of the ACAP3 Gene as Molecular Biomarker of Epilepsy. Sex Differences in Seizure Types and Symptoms.
  2. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  3. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
  4. minisatellite locus UPS29 can regulate an activity of CENTB5, SCNN1D and ACOT7 in nervous system cells.
    Title: [CENTB5 gene expression in human and mouse].
Submit: New GeneRIF Correction

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA1716

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables GTPase activator activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in neuron migration IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of neuron projection development IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in growth cone IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 3
Names
centaurin-beta-5
cnt-b5

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.

mRNA and Protein(s)

  1. NM_030649.3 → NP_085152.2  arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 3

    See identical proteins and their annotated locations for NP_085152.2

    Status: VALIDATED

    Source sequence(s)
    AB051503, AL139287, BC051194
    Consensus CDS
    CCDS19.2
    UniProtKB/Swiss-Prot
    B1AMF5, Q5TA42, Q5TA43, Q86UT3, Q96P50, Q9BSR9, Q9C0E7
    Related
    ENSP00000346733.5, ENST00000354700.10
    Conserved Domains (7) summary
    cd07637
    Location:16 → 215
    BAR_ACAP3; The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with Coiled-coil, ANK repeat and PH domain containing protein 3
    cd00204
    Location:701 → 788
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cd13250
    Location:271 → 367
    PH_ACAP; ArfGAP with coiled-coil, ankyrin repeat and PH domains Pleckstrin homology (PH) domain
    pfam00169
    Location:269 → 363
    PH; PH domain
    pfam01412
    Location:403 → 521
    ArfGap; Putative GTPase activating protein for Arf
    pfam13637
    Location:705 → 756
    Ank_4; Ankyrin repeats (many copies)
    sd00045
    Location:702 → 733
    ANK; ANK repeat [structural motif]

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

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    1292391..1307930 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005244715.3 → XP_005244772.1  arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 3 isoform X6

    Related
    ENSP00000321139.4, ENST00000353662.4
    Conserved Domains (7) summary
    cd00204
    Location:668 → 755
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cd13250
    Location:271 → 367
    PH_ACAP; ArfGAP with coiled-coil, ankyrin repeat and PH domains Pleckstrin homology (PH) domain
    pfam00169
    Location:269 → 363
    PH; PH domain
    pfam01412
    Location:403 → 521
    ArfGap; Putative GTPase activating protein for Arf
    pfam13637
    Location:672 → 723
    Ank_4; Ankyrin repeats (many copies)
    sd00045
    Location:669 → 700
    ANK; ANK repeat [structural motif]
    cl12013
    Location:16 → 215
    BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

  2. XM_011540608.3 → XP_011538910.1  arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 3 isoform X4

    Conserved Domains (7) summary
    cd00204
    Location:679 → 766
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cd13250
    Location:249 → 345
    PH_ACAP; ArfGAP with coiled-coil, ankyrin repeat and PH domains Pleckstrin homology (PH) domain
    pfam00169
    Location:247 → 341
    PH; PH domain
    pfam01412
    Location:381 → 499
    ArfGap; Putative GTPase activating protein for Arf
    pfam13637
    Location:683 → 734
    Ank_4; Ankyrin repeats (many copies)
    sd00045
    Location:680 → 711
    ANK; ANK repeat [structural motif]
    cl12013
    Location:16 → 200
    BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

  3. XM_011540609.3 → XP_011538911.1  arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 3 isoform X5

    Conserved Domains (7) summary
    cd00204
    Location:678 → 765
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cd13250
    Location:281 → 377
    PH_ACAP; ArfGAP with coiled-coil, ankyrin repeat and PH domains Pleckstrin homology (PH) domain
    pfam00169
    Location:279 → 373
    PH; PH domain
    pfam01412
    Location:413 → 531
    ArfGap; Putative GTPase activating protein for Arf
    pfam13637
    Location:682 → 733
    Ank_4; Ankyrin repeats (many copies)
    sd00045
    Location:679 → 710
    ANK; ANK repeat [structural motif]
    cl12013
    Location:16 → 225
    BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

  4. XM_011540606.3 → XP_011538908.1  arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 3 isoform X1

    Conserved Domains (7) summary
    cd00204
    Location:711 → 798
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cd13250
    Location:281 → 377
    PH_ACAP; ArfGAP with coiled-coil, ankyrin repeat and PH domains Pleckstrin homology (PH) domain
    pfam00169
    Location:279 → 373
    PH; PH domain
    pfam01412
    Location:413 → 531
    ArfGap; Putative GTPase activating protein for Arf
    pfam13637
    Location:715 → 766
    Ank_4; Ankyrin repeats (many copies)
    sd00045
    Location:712 → 743
    ANK; ANK repeat [structural motif]
    cl12013
    Location:16 → 225
    BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

  5. XM_024452993.2 → XP_024308761.1  arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 3 isoform X3

    Conserved Domains (5) summary
    cd07637
    Location:16 → 215
    BAR_ACAP3; The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with Coiled-coil, ANK repeat and PH domain containing protein 3
    cd00204
    Location:701 → 788
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cd13250
    Location:271 → 367
    PH_ACAP; ArfGAP with coiled-coil, ankyrin repeat and PH domains Pleckstrin homology (PH) domain
    sd00045
    Location:702 → 733
    ANK; ANK repeat [structural motif]
    pfam01412
    Location:403 → 521
    ArfGap; Putative GTPase activating protein for Arf

  6. XM_011540607.2 → XP_011538909.1  arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 3 isoform X2

    Conserved Domains (7) summary
    cd00204
    Location:711 → 798
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    cd13250
    Location:281 → 377
    PH_ACAP; ArfGAP with coiled-coil, ankyrin repeat and PH domains Pleckstrin homology (PH) domain
    pfam00169
    Location:279 → 373
    PH; PH domain
    pfam01412
    Location:413 → 531
    ArfGap; Putative GTPase activating protein for Arf
    pfam13637
    Location:715 → 766
    Ank_4; Ankyrin repeats (many copies)
    sd00045
    Location:712 → 743
    ANK; ANK repeat [structural motif]
    cl12013
    Location:16 → 225
    BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

  7. XM_005244717.4 → XP_005244774.1  arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 3 isoform X7

    Conserved Domains (5) summary
    cd00204
    Location:360 → 447
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    pfam01412
    Location:62 → 180
    ArfGap; Putative GTPase activating protein for Arf
    pfam13637
    Location:364 → 415
    Ank_4; Ankyrin repeats (many copies)
    sd00045
    Location:361 → 392
    ANK; ANK repeat [structural motif]
    cl17171
    Location:1 → 26
    PH-like; Pleckstrin homology-like domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    723917..739479 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054334177.1 → XP_054190152.1  arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 3 isoform X6

  2. XM_054334175.1 → XP_054190150.1  arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 3 isoform X4

  3. XM_054334176.1 → XP_054190151.1  arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 3 isoform X5

  4. XM_054334172.1 → XP_054190147.1  arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 3 isoform X1

  5. XM_054334174.1 → XP_054190149.1  arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 3 isoform X3

  6. XM_054334173.1 → XP_054190148.1  arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 3 isoform X2

  7. XM_054334178.1 → XP_054190153.1  arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 3 isoform X7

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96P50.2 GenPept UniProtKB/Swiss-Prot:Q96P50

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