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ASAP3 ArfGAP with SH3 domain, ankyrin repeat and PH domain 3 [ Homo sapiens (human) ]

Gene ID: 55616, updated on 26-Nov-2024

Summary

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Official Symbol
ASAP3provided by HGNC
Official Full Name
ArfGAP with SH3 domain, ankyrin repeat and PH domain 3provided by HGNC
Primary source
HGNC:HGNC:14987
See related
Ensembl:ENSG00000088280 MIM:616594; AllianceGenome:HGNC:14987
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
ACAP4; UPLC1; CENTB6; DDEFL1
Summary
This gene encodes a member of a subfamily of ADP-ribosylation factor(Arf) GTPase-activating proteins that contain additional ankyrin repeat and pleckstrin homology domains. The Arf GAP domain of this protein catalyzes the hydrolysis of GTP bound to Arf proteins. The encoded protein promotes cell differentiation and migration and has been implicated in cancer cell invasion. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2009]
Expression
Ubiquitous expression in ovary (RPKM 21.1), skin (RPKM 19.0) and 23 other tissues See more
Orthologs
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Genomic context

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See ASAP3 in Genome Data Viewer
Location:
1p36.12
Exon count:
26
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (23428563..23484631, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (23263051..23319108, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (23755056..23810672, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 360 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 361 Neighboring gene NANOG hESC enhancer GRCh37_chr1:23697210-23697795 Neighboring gene ZNF436 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 9848 Neighboring gene zinc finger protein 436 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 362 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:23709609-23709825 Neighboring gene transcription elongation factor A3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 363 Neighboring gene NANOG hESC enhancer GRCh37_chr1:23745635-23746193 Neighboring gene uncharacterized LOC124903875 Neighboring gene Sharpr-MPRA regulatory region 12987 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:23800831-23801332 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:23801333-23801832 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 412 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 413 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 364 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 414 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:23829854-23830688 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:23830689-23831522 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:23847293-23848492 Neighboring gene uncharacterized LOC101928163 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:23854779-23854975 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 365 Neighboring gene E2F transcription factor 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:23857131-23857279 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 415 Neighboring gene Sharpr-MPRA regulatory region 6048 Neighboring gene uncharacterized LOC124903876 Neighboring gene Sharpr-MPRA regulatory region 7496 Neighboring gene uncharacterized LOC105376859 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:23875384-23875934 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 416

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. Isolation of development and differentiation enhancing factor-like 1 (DDEFL1) as a drug target for hepatocellular carcinomas. Okabe H, et al. Int J Oncol, 2004 Jan. PMID 14654939
  2. Phosphorylation of the Bin, Amphiphysin, and RSV161/167 (BAR) domain of ACAP4 regulates membrane tubulation. Zhao X, et al. Proc Natl Acad Sci U S A, 2013 Jul 2. PMID 23776207, Free PMC Article
  3. ASAP3 expression in non-small cell lung cancer: association with cancer development and patients' clinical outcome. Fan C, et al. Tumour Biol, 2014 Feb. PMID 24078447
  4. The structure of an Arf-ArfGAP complex reveals a Ca2+ regulatory mechanism. Ismail SA, et al. Cell, 2010 May 28. PMID 20510928
  5. Acetylation of ACAP4 regulates CCL18-elicited breast cancer cell migration and invasion. Song X, et al. J Mol Cell Biol, 2018 Dec 1. PMID 30395269, Free PMC Article

See all (33) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. ACAP4 physically interacts with CrkII. Functional characterization showed that the interaction is required for the recruitment of ACAP4 to the plasma membrane where ACAP4 functions to regulate the recycling of the signal transducer integrin beta1.
    Title: ACAP4 interacts with CrkII to promote the recycling of integrin β1.
  2. ARF6 GTPase-activating protein ACAP4 regulates CCL18-elicited breast cancer cell migration via the acetyltransferase PCAF-mediated acetylation. CCL18 stimulation elicited breast cancer cell migration and invasion via PCAF-dependent acetylation.
    Title: Acetylation of ACAP4 regulates CCL18-elicited breast cancer cell migration and invasion.
  3. MiR-143-3p acts as an anti-oncogene by downregulating ITGA6/ASAP3 protein expression and could offer new insight into potential therapeutic targets for CRC.
    Title: MicroRNA-143-3p inhibits colorectal cancer metastases by targeting ITGA6 and ASAP3.
  4. Results show that ASAP3 was amplified in colorectal cancer (CRC) tissues, and its upregulation was associated with poor prognosis of patients with CRC. Also, it promoted growth of colon tumors, and accelerated cell invasion and migration through its binding to NEMO. These results suggest that ASAP3 acts as an oncogene.
    Title: Upregulation of ASAP3 contributes to colorectal carcinogenesis and indicates poor survival outcome.
  5. The data, for the first time, link ASAP3 with ACTG1 in the regulation of cytoskeletal maintenance and cell motility
    Title: Loss of ASAP3 destabilizes cytoskeletal protein ACTG1 to suppress cancer cell migration.
  6. ). These data indicate that ASAP3 is elevated in NSCLC and may contribute to cancer development and patients' poor clinical outcome, which is possibly due to its critical roles in regulating cancer invasion.
    Title: ASAP3 expression in non-small cell lung cancer: association with cancer development and patients' clinical outcome.
  7. Phosphorylation of the N-terminal region of ACAP4 (named the Bin, Amphiphysin, and RSV161/167[BAR] domain at Tyr34) is necessary for epidermal growth factor (EGF)-elicited membrane remodeling.
    Title: Phosphorylation of the Bin, Amphiphysin, and RSV161/167 (BAR) domain of ACAP4 regulates membrane tubulation.
  8. ACAP4 protein cooperates with Grb2 protein to orchestrate epidermal growth factor-stimulated integrin beta1 recycling in cell migration
    Title: ACAP4 protein cooperates with Grb2 protein to orchestrate epidermal growth factor-stimulated integrin β1 recycling in cell migration.
  9. The ArfGAP catalytic mechanism and shows a glutamine from Arf6 and an arginine fingerASAP3 as the important catalytic residues; unexpectedly the structure shows a calcium ion, liganded by both proteins in the complex interface.
    Title: The structure of an Arf-ArfGAP complex reveals a Ca2+ regulatory mechanism.
  10. ASAP3 functions nonredundantly with ASAP1 to control cell movement and may have a role in cancer cell invasion.
    Title: ASAP3 is a focal adhesion-associated Arf GAP that functions in cell migration and invasion.
Submit: New GeneRIF Correction See all GeneRIFs (11)

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

EBI GWAS Catalog

Description
Discovery and refinement of loci associated with lipid levels.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables GTPase activator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables GTPase activator activity IDA
Inferred from Direct Assay
more info
 PubMed 
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 cell migration IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of GTPase activity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of stress fiber assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of stress fiber assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in cytosol IDA
Inferred from Direct Assay
more info
  
is_active_in focal adhesion IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in focal adhesion IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in intracellular membrane-bounded organelle IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in ruffle IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in ruffle IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3
Names
ARF6 GTPase-activating protein
ArfGAP with SH3 domain, ankyrin repeat and PH domain 3 1
centaurin, beta 6
development and differentiation enhancing factor-like 1
protein up-regulated in liver cancer 1
up-regulated in liver cancer 1 (UPLC1)

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_001143778.2 → NP_001137250.1  arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3 isoform b

    See identical proteins and their annotated locations for NP_001137250.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon in the coding region and uses an alternate in-frame splice site compared to variant 1. The resulting protein (isoform b) is shorter compared to isoform a.
    Source sequence(s)
    AK000206, AK295100, AL021154, AL357134
    Consensus CDS
    CCDS44087.1
    UniProtKB/Swiss-Prot
    Q8TDY4
    Related
    ENSP00000408826.2, ENST00000437606.6
    Conserved Domains (7) summary
    cd07640
    Location:35 → 234
    BAR_ASAP3; The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with SH3 domain, ANK repeat and PH domain containing protein 3
    cd00204
    Location:581 → 665
    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 ...
    cd13251
    Location:285 → 391
    PH_ASAP; ArfGAP with SH3 domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain
    pfam00169
    Location:298 → 381
    PH; PH domain
    pfam01412
    Location:419 → 534
    ArfGap; Putative GTPase activating protein for Arf
    pfam13857
    Location:599 → 653
    Ank_5; Ankyrin repeats (many copies)
    sd00045
    Location:542 → 575
    ANK; ANK repeat [structural motif]

  2. NM_017707.4 → NP_060177.2  arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3 isoform a

    See identical proteins and their annotated locations for NP_060177.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (a).
    Source sequence(s)
    AB056749, AK000206, AL021154, AL357134
    Consensus CDS
    CCDS235.1
    UniProtKB/Swiss-Prot
    B3KRW0, B4DHH4, Q6P9F4, Q86UY1, Q8TDY4, Q9NXK2
    Related
    ENSP00000338769.3, ENST00000336689.8
    Conserved Domains (7) summary
    cd07640
    Location:35 → 243
    BAR_ASAP3; The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with SH3 domain, ANK repeat and PH domain containing protein 3
    cd00204
    Location:590 → 674
    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 ...
    cd13251
    Location:294 → 400
    PH_ASAP; ArfGAP with SH3 domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain
    pfam00169
    Location:307 → 390
    PH; PH domain
    pfam01412
    Location:428 → 543
    ArfGap; Putative GTPase activating protein for Arf
    pfam13857
    Location:608 → 662
    Ank_5; Ankyrin repeats (many copies)
    sd00045
    Location:551 → 584
    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
    23428563..23484631 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017001687.1 → XP_016857176.1  arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3 isoform X4

  2. XM_047424481.1 → XP_047280437.1  arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3 isoform X7

    UniProtKB/TrEMBL
    A0AAA9YHE6
    Related
    ENSP00000518744.1, ENST00000711427.1

  3. XM_017001688.3 → XP_016857177.1  arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3 isoform X5

    UniProtKB/TrEMBL
    B4DRP2
    Conserved Domains (7) summary
    cd00204
    Location:459 → 543
    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 ...
    cd13251
    Location:163 → 269
    PH_ASAP; ArfGAP with SH3 domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain
    pfam00169
    Location:176 → 259
    PH; PH domain
    pfam01412
    Location:297 → 412
    ArfGap; Putative GTPase activating protein for Arf
    pfam13857
    Location:477 → 531
    Ank_5; Ankyrin repeats (many copies)
    sd00045
    Location:420 → 453
    ANK; ANK repeat [structural motif]
    cl12013
    Location:1 → 112
    BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

  4. XM_017001689.2 → XP_016857178.1  arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3 isoform X6

  5. XM_017001685.3 → XP_016857174.1  arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3 isoform X2

  6. XM_017001686.3 → XP_016857175.1  arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3 isoform X3

  7. XM_011541755.3 → XP_011540057.1  arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3 isoform X1

    Conserved Domains (7) summary
    cd07640
    Location:35 → 243
    BAR_ASAP3; The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with SH3 domain, ANK repeat and PH domain containing protein 3
    cd00204
    Location:592 → 676
    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 ...
    cd13251
    Location:296 → 402
    PH_ASAP; ArfGAP with SH3 domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain
    pfam00169
    Location:309 → 392
    PH; PH domain
    pfam01412
    Location:430 → 545
    ArfGap; Putative GTPase activating protein for Arf
    pfam13857
    Location:610 → 664
    Ank_5; Ankyrin repeats (many copies)
    sd00045
    Location:553 → 586
    ANK; ANK repeat [structural motif]

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_014040926.1 Reference GRCh38.p14 PATCHES

    Range
    198542..254610 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331922.1 → XP_054187897.1  arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3 isoform X4

  2. XM_054331925.1 → XP_054187900.1  arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3 isoform X7

    UniProtKB/TrEMBL
    A0AAA9YHE6

  3. XM_054331923.1 → XP_054187898.1  arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3 isoform X5

    UniProtKB/TrEMBL
    B4DRP2

  4. XM_054331924.1 → XP_054187899.1  arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3 isoform X6

  5. XM_054331920.1 → XP_054187895.1  arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3 isoform X2

  6. XM_054331921.1 → XP_054187896.1  arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3 isoform X3

  7. XM_054331919.1 → XP_054187894.1  arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    23263051..23319108 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054337532.1 → XP_054193507.1  arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3 isoform X4

  2. XM_054337535.1 → XP_054193510.1  arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3 isoform X7

    UniProtKB/TrEMBL
    A0AAA9YHE6

  3. XM_054337533.1 → XP_054193508.1  arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3 isoform X5

    UniProtKB/TrEMBL
    B4DRP2

  4. XM_054337534.1 → XP_054193509.1  arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3 isoform X6

  5. XM_054337530.1 → XP_054193505.1  arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3 isoform X2

  6. XM_054337531.1 → XP_054193506.1  arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3 isoform X3

  7. XM_054337529.1 → XP_054193504.1  arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 3 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8TDY4.1 GenPept UniProtKB/Swiss-Prot:Q8TDY4

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