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ARHGAP39 Rho GTPase activating protein 39 [ Homo sapiens (human) ]

Gene ID: 80728, updated on 3-Apr-2024

Summary

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Official Symbol
ARHGAP39provided by HGNC
Official Full Name
Rho GTPase activating protein 39provided by HGNC
Primary source
HGNC:HGNC:29351
See related
Ensembl:ENSG00000147799 MIM:615880; AllianceGenome:HGNC:29351
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
CrGAP; Vilse
Summary
Predicted to enable GTPase activator activity. Involved in postsynapse organization. Is active in glutamatergic synapse. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis (RPKM 5.1), brain (RPKM 1.6) and 17 other tissues See more
Orthologs
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Genomic context

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Location:
8q24.3
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (144529179..144700362, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (145699369..145873884, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (145754563..145911231, complement)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19699 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19700 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145746055-145746717 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:145747722-145747910 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19702 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145749372-145750034 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145750035-145750697 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145751430-145752286 Neighboring gene Sharpr-MPRA regulatory region 11949 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19706 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19707 Neighboring gene leucine rich repeat containing 14 Neighboring gene leucine rich repeat containing 24 Neighboring gene chromosome 8 open reading frame 82 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:145795054-145796253 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145816391-145816972 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145816973-145817554 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145879634-145880145 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145880146-145880656 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145899251-145899750 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145909098-145909710 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145909711-145910323 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145910937-145911548 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145912735-145913607 Neighboring gene Sharpr-MPRA regulatory region 12231 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145918540-145919362 Neighboring gene uncharacterized LOC100996662 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:145926819-145928018 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145959413-145960300 Neighboring gene uncharacterized LOC107986986 Neighboring gene zinc finger protein 251

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. ARHGAP39 is a prognostic biomarker involved in immune infiltration in breast cancer. Yao L, et al. BMC Cancer, 2023 May 15. PMID 37189064, Free PMC Article
  2. Biological function analysis of ARHGAP39 as an independent prognostic biomarker in hepatocellular carcinoma. Ding Y, et al. Aging (Albany NY), 2023 Apr 5. PMID 37059586, Free PMC Article
  3. The CNK2 scaffold interacts with vilse and modulates Rac cycling during spine morphogenesis in hippocampal neurons. Lim J, et al. Curr Biol, 2014 Mar 31. PMID 24656827, Free PMC Article
  4. Cross GTPase-activating protein (CrossGAP)/Vilse links the Roundabout receptor to Rac to regulate midline repulsion. Hu H, et al. Proc Natl Acad Sci U S A, 2005 Mar 22. PMID 15755809, Free PMC Article
  5. Genome-wide association study of smoking behaviours among Bangladeshi adults. Argos M, et al. J Med Genet, 2014 May. PMID 24665060, Free PMC Article

See all (31) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. ARHGAP39 is a prognostic biomarker involved in immune infiltration in breast cancer.
    Title: ARHGAP39 is a prognostic biomarker involved in immune infiltration in breast cancer.
  2. Biological function analysis of ARHGAP39 as an independent prognostic biomarker in hepatocellular carcinoma.
    Title: Biological function analysis of ARHGAP39 as an independent prognostic biomarker in hepatocellular carcinoma.
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

EBI GWAS Catalog

Description
Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.
EBI GWAS Catalog
Genome-wide association study of smoking behaviours among Bangladeshi adults.
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)

Genotypes

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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Homology

Clone Names

  • KIAA1688

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 TAS
Traceable Author Statement
more info
  
Process Evidence Code Pubs
involved_in postsynapse organization IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in postsynapse organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of small GTPase mediated signal transduction TAS
Traceable Author Statement
more info
  
involved_in signal transduction IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoskeleton IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
is_active_in glutamatergic synapse IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in glutamatergic synapse IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
rho GTPase-activating protein 39
Names
RhoGAP93B homolog
crossGAP homolog

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_001308207.1 → NP_001295136.1  rho GTPase-activating protein 39 isoform 1

    See identical proteins and their annotated locations for NP_001295136.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the shorter isoform (1). Both variants 1 and 2 encode the same isoform.
    Source sequence(s)
    AB051475
    Consensus CDS
    CCDS78374.1
    UniProtKB/Swiss-Prot
    B4E1I1, Q9C0H5
    UniProtKB/TrEMBL
    B4DK23
    Conserved Domains (3) summary
    cd04389
    Location:888 → 1073
    RhoGAP_KIAA1688; RhoGAP_KIAA1688: GTPase-activator protein (GAP) domain for Rho-like GTPases found in KIAA1688-like proteins; KIAA1688 is a protein of unknown function that contains a RhoGAP domain and a myosin tail homology 4 (MyTH4) domain. Small GTPases cluster into ...
    pfam00397
    Location:69 → 95
    WW; WW domain
    pfam00784
    Location:767 → 876
    MyTH4; MyTH4 domain

  2. NM_001308208.2 → NP_001295137.1  rho GTPase-activating protein 39 isoform 1

    See identical proteins and their annotated locations for NP_001295137.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AB051475, AF186192, AK296353, DA118202
    Consensus CDS
    CCDS78374.1
    UniProtKB/Swiss-Prot
    B4E1I1, Q9C0H5
    UniProtKB/TrEMBL
    B4DK23
    Related
    ENSP00000276826.5, ENST00000276826.5
    Conserved Domains (3) summary
    cd04389
    Location:888 → 1073
    RhoGAP_KIAA1688; RhoGAP_KIAA1688: GTPase-activator protein (GAP) domain for Rho-like GTPases found in KIAA1688-like proteins; KIAA1688 is a protein of unknown function that contains a RhoGAP domain and a myosin tail homology 4 (MyTH4) domain. Small GTPases cluster into ...
    pfam00397
    Location:69 → 95
    WW; WW domain
    pfam00784
    Location:767 → 876
    MyTH4; MyTH4 domain

  3. NM_025251.3 → NP_079527.1  rho GTPase-activating protein 39 isoform 2

    See identical proteins and their annotated locations for NP_079527.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, and includes an alternate in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (2) is longer than isoform 1.
    Source sequence(s)
    AC084125, AF186192, KF573657
    Consensus CDS
    CCDS34971.1
    UniProtKB/TrEMBL
    A0A2X0SSG1
    Related
    ENSP00000366522.2, ENST00000377307.7
    Conserved Domains (3) summary
    cd04389
    Location:919 → 1104
    RhoGAP_KIAA1688; RhoGAP_KIAA1688: GTPase-activator protein (GAP) domain for Rho-like GTPases found in KIAA1688-like proteins; KIAA1688 is a protein of unknown function that contains a RhoGAP domain and a myosin tail homology 4 (MyTH4) domain. Small GTPases cluster into ...
    pfam00397
    Location:69 → 95
    WW; WW domain
    pfam00784
    Location:767 → 907
    MyTH4; MyTH4 domain

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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    144529179..144700362 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011517308.2 → XP_011515610.1  rho GTPase-activating protein 39 isoform X1

    See identical proteins and their annotated locations for XP_011515610.1

    UniProtKB/TrEMBL
    A0A2X0SSG1
    Conserved Domains (3) summary
    cd04389
    Location:919 → 1104
    RhoGAP_KIAA1688; RhoGAP_KIAA1688: GTPase-activator protein (GAP) domain for Rho-like GTPases found in KIAA1688-like proteins; KIAA1688 is a protein of unknown function that contains a RhoGAP domain and a myosin tail homology 4 (MyTH4) domain. Small GTPases cluster into ...
    pfam00397
    Location:69 → 95
    WW; WW domain
    pfam00784
    Location:767 → 907
    MyTH4; MyTH4 domain

  2. XM_017013870.3 → XP_016869359.1  rho GTPase-activating protein 39 isoform X1

    UniProtKB/TrEMBL
    A0A2X0SSG1
    Conserved Domains (3) summary
    cd04389
    Location:919 → 1104
    RhoGAP_KIAA1688; RhoGAP_KIAA1688: GTPase-activator protein (GAP) domain for Rho-like GTPases found in KIAA1688-like proteins; KIAA1688 is a protein of unknown function that contains a RhoGAP domain and a myosin tail homology 4 (MyTH4) domain. Small GTPases cluster into ...
    pfam00397
    Location:69 → 95
    WW; WW domain
    pfam00784
    Location:767 → 907
    MyTH4; MyTH4 domain

  3. XM_011517312.2 → XP_011515614.1  rho GTPase-activating protein 39 isoform X2

    UniProtKB/TrEMBL
    A0A2X0SSG1
    Conserved Domains (2) summary
    cd04389
    Location:762 → 947
    RhoGAP_KIAA1688; RhoGAP_KIAA1688: GTPase-activator protein (GAP) domain for Rho-like GTPases found in KIAA1688-like proteins; KIAA1688 is a protein of unknown function that contains a RhoGAP domain and a myosin tail homology 4 (MyTH4) domain. Small GTPases cluster into ...
    pfam00784
    Location:610 → 750
    MyTH4; MyTH4 domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    145699369..145873884 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054361292.1 → XP_054217267.1  rho GTPase-activating protein 39 isoform X1

  2. XM_054361291.1 → XP_054217266.1  rho GTPase-activating protein 39 isoform X1

  3. XM_054361293.1 → XP_054217268.1  rho GTPase-activating protein 39 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9C0H5.2 GenPept UniProtKB/Swiss-Prot:Q9C0H5

Gene LinkOut

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