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

    Gene ID: 116983, updated on 2-Nov-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 act upstream of or within neuron migration and regulation of neuron projection development. Predicted to be located in endosome membrane and growth cone. [provided by Alliance of Genome Resources, Nov 2024]
    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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    See ACAP3 in Genome Data Viewer
    Location:
    1p36.33
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (1292391..1307930, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (723917..739479, complement)
    RS_2024_09 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 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 negatively regulated by HDAC2 inhibits the malignant development of papillary thyroid carcinoma cells. Zhan F, et al. Int J Biochem Cell Biol, 2024 Sep. PMID 39098591
    4. 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
    5. 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

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ACAP3 negatively regulated by HDAC2 inhibits the malignant development of papillary thyroid carcinoma cells.
      Title: ACAP3 negatively regulated by HDAC2 inhibits the malignant development of papillary thyroid carcinoma cells.
    2. 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.
    3. 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.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    5. 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
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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_2024_08

    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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