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

    Gene ID: 80728, updated on 10-Dec-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, Dec 2024]
    Expression
    Broad expression in testis (RPKM 5.1), brain (RPKM 1.6) and 17 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ARHGAP39 in Genome Data Viewer
    Location:
    8q24.3
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (144529179..144700362, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (145699369..145873884, complement)
    RS_2024_09 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. A homozygous variant in ARHGAP39 is associated with lethal cerebellar vermis hypoplasia in a consanguineous Saudi family. Alayoubi AM, et al. Sci Rep, 2024 Oct 25. PMID 39455833, Free PMC Article
    2. 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
    3. 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
    4. 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
    5. 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

    See all (34) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A homozygous variant in ARHGAP39 is associated with lethal cerebellar vermis hypoplasia in a consanguineous Saudi family.
      Title: A homozygous variant in ARHGAP39 is associated with lethal cerebellar vermis hypoplasia in a consanguineous Saudi family.
    2. 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.
    3. 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)

    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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    NEW Try the new Transcript table

    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_2024_08

    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

      UniProtKB/TrEMBL
      A0A2X0SSG1

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

      UniProtKB/TrEMBL
      A0A2X0SSG1

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

      UniProtKB/TrEMBL
      A0A2X0SSG1
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9C0H5.2 GenPept UniProtKB/Swiss-Prot:Q9C0H5

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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