Aliases for ARHGAP39 Gene

Aliases for ARHGAP39 Gene

  • Rho GTPase Activating Protein 39 2 3 5
  • Rho GTPase-Activating Protein 39 3 4
  • KIAA1688 2 4
  • CrGAP 2 3
  • Vilse 2 3
  • RhoGAP93B Homolog (Drosophila) 2
  • CrossGAP Homolog (Drosophila) 2
  • RhoGAP93B Homolog 3
  • CrossGAP Homolog 3
  • ARHGAP39 5

External Ids for ARHGAP39 Gene

Previous GeneCards Identifiers for ARHGAP39 Gene

  • GC08M145754
  • GC08M140868

Summaries for ARHGAP39 Gene

GeneCards Summary for ARHGAP39 Gene

ARHGAP39 (Rho GTPase Activating Protein 39) is a Protein Coding gene. Diseases associated with ARHGAP39 include Charcot-Marie-Tooth Disease, X-Linked Recessive, 3 and Neuronopathy, Distal Hereditary Motor, Type I. Among its related pathways are Signaling by GPCR and Signaling by Robo receptor.

Additional gene information for ARHGAP39 Gene

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ARHGAP39 Gene

Genomics for ARHGAP39 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for ARHGAP39 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ARHGAP39 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ARHGAP39

Genomic Locations for ARHGAP39 Gene

Genomic Locations for ARHGAP39 Gene
171,342 bases
Minus strand
156,632 bases
Minus strand

Genomic View for ARHGAP39 Gene

Genes around ARHGAP39 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ARHGAP39 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ARHGAP39 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ARHGAP39 Gene

Proteins for ARHGAP39 Gene

  • Protein details for ARHGAP39 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Rho GTPase-activating protein 39
    Protein Accession:
    Secondary Accessions:
    • B4E1I1

    Protein attributes for ARHGAP39 Gene

    1083 amino acids
    Molecular mass:
    121286 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAB21779.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305}; Sequence=BAG64793.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for ARHGAP39 Gene


neXtProt entry for ARHGAP39 Gene

Post-translational modifications for ARHGAP39 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for ARHGAP39 Gene

Antibody Products

  • Boster Bio Antibodies for ARHGAP39

No data available for DME Specific Peptides for ARHGAP39 Gene

Domains & Families for ARHGAP39 Gene

Gene Families for ARHGAP39 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for ARHGAP39 Gene

  • RhoGAP domain
  • Core domain in kinesin and myosin motor

Suggested Antigen Peptide Sequences for ARHGAP39 Gene

GenScript: Design optimal peptide antigens:
  • KIAA1688 protein (Q6PJQ0_HUMAN)
  • Rho GTPase-activating protein 39 (RHG39_HUMAN)
genes like me logo Genes that share domains with ARHGAP39: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for ARHGAP39 Gene

Function for ARHGAP39 Gene

Phenotypes From GWAS Catalog for ARHGAP39 Gene

Gene Ontology (GO) - Molecular Function for ARHGAP39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005096 GTPase activator activity IBA 21873635
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with ARHGAP39: view
genes like me logo Genes that share phenotypes with ARHGAP39: view

Animal Model Products

CRISPR Products

miRNA for ARHGAP39 Gene

miRTarBase miRNAs that target ARHGAP39

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ARHGAP39

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ARHGAP39 Gene

Localization for ARHGAP39 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ARHGAP39 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ARHGAP39 gene
Compartment Confidence
cytosol 5
nucleus 4
cytoskeleton 3
plasma membrane 1
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytokinetic bridge (2)
  • Cytosol (2)
  • Microtubules (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ARHGAP39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IBA 21873635
GO:0005829 cytosol TAS --
GO:0005856 cytoskeleton IEA --
GO:0098978 glutamatergic synapse IMP 24656827
genes like me logo Genes that share ontologies with ARHGAP39: view

Pathways & Interactions for ARHGAP39 Gene

genes like me logo Genes that share pathways with ARHGAP39: view

Pathways by source for ARHGAP39 Gene

SIGNOR curated interactions for ARHGAP39 Gene


Gene Ontology (GO) - Biological Process for ARHGAP39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007165 signal transduction IEA --
GO:0043547 positive regulation of GTPase activity IEA --
GO:0051056 regulation of small GTPase mediated signal transduction TAS --
GO:0099173 postsynapse organization IMP 24656827
genes like me logo Genes that share ontologies with ARHGAP39: view

Drugs & Compounds for ARHGAP39 Gene

No Compound Related Data Available

Transcripts for ARHGAP39 Gene

mRNA/cDNA for ARHGAP39 Gene

6 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ARHGAP39

Alternative Splicing Database (ASD) splice patterns (SP) for ARHGAP39 Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10
SP1: -

Relevant External Links for ARHGAP39 Gene

GeneLoc Exon Structure for

Expression for ARHGAP39 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ARHGAP39 Gene

mRNA differential expression in normal tissues according to GTEx for ARHGAP39 Gene

This gene is overexpressed in Nerve - Tibial (x4.6) and Testis (x4.1).

Protein differential expression in normal tissues from HIPED for ARHGAP39 Gene

This gene is overexpressed in Frontal cortex (23.5), Lung (14.2), Retina (10.0), Fetal Brain (9.7), and Testis (6.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ARHGAP39 Gene

Protein tissue co-expression partners for ARHGAP39 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ARHGAP39

SOURCE GeneReport for Unigene cluster for ARHGAP39 Gene:


Evidence on tissue expression from TISSUES for ARHGAP39 Gene

  • Nervous system(4.6)
genes like me logo Genes that share expression patterns with ARHGAP39: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for ARHGAP39 Gene

Orthologs for ARHGAP39 Gene

This gene was present in the common ancestor of animals.

Orthologs for ARHGAP39 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ARHGAP39 30 31
  • 98.5 (n)
(Bos Taurus)
Mammalia ARHGAP39 30 31
  • 87.22 (n)
(Monodelphis domestica)
Mammalia ARHGAP39 31
  • 87 (a)
(Canis familiaris)
Mammalia ARHGAP39 30 31
  • 86.19 (n)
(Mus musculus)
Mammalia Arhgap39 30 17 31
  • 84.67 (n)
(Rattus norvegicus)
Mammalia Arhgap39 30
  • 84.34 (n)
(Ornithorhynchus anatinus)
Mammalia ARHGAP39 31
  • 79 (a)
(Gallus gallus)
Aves ARHGAP39 31
  • 72 (a)
(Anolis carolinensis)
Reptilia ARHGAP39 31
  • 77 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.29319 30
(Danio rerio)
Actinopterygii LOC101884459 30
  • 70.14 (n)
arhgap39 31
  • 66 (a)
Dr.27236 30
Fruit Fly
(Drosophila melanogaster)
Insecta RhoGAP93B 31
  • 29 (a)
(Caenorhabditis elegans)
Secernentea Y92H12BM.1 31
  • 38 (a)
Y92H12BL.4 31
  • 34 (a)
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.2763 31
  • 62 (a)
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.3354 30
Species where no ortholog for ARHGAP39 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)

Evolution for ARHGAP39 Gene

Gene Tree for ARHGAP39 (if available)
Gene Tree for ARHGAP39 (if available)
Evolutionary constrained regions (ECRs) for ARHGAP39: view image

Paralogs for ARHGAP39 Gene

(1) SIMAP similar genes for ARHGAP39 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with ARHGAP39: view

No data available for Paralogs for ARHGAP39 Gene

Variants for ARHGAP39 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ARHGAP39 Gene

SNP ID Clinical significance and condition Chr 08 pos Variation AA Info Type
787883 Benign: not provided 144,545,316(-) G/A SYNONYMOUS_VARIANT
787884 Benign: not provided 144,548,405(-) G/C SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for ARHGAP39 Gene

Structural Variations from Database of Genomic Variants (DGV) for ARHGAP39 Gene

Variant ID Type Subtype PubMed ID
dgv1207n67 CNV gain 20364138
dgv1242e201 CNV deletion 23290073
dgv1243e201 CNV deletion 23290073
dgv12444n54 CNV loss 21841781
dgv1244e201 CNV deletion 23290073
dgv1245e201 CNV deletion 23290073
dgv4271e59 CNV duplication 20981092
esv1009938 CNV deletion 20482838
esv1114154 CNV insertion 17803354
esv1657415 CNV insertion 17803354
esv22509 CNV loss 19812545
esv23002 CNV loss 19812545
esv23868 CNV gain+loss 19812545
esv2666702 CNV deletion 23128226
esv2667076 CNV deletion 23128226
esv2670099 CNV deletion 23128226
esv2674311 CNV deletion 23128226
esv2738069 CNV deletion 23290073
esv2738072 CNV deletion 23290073
esv2738075 CNV deletion 23290073
esv2738076 CNV deletion 23290073
esv2738077 CNV deletion 23290073
esv2738078 CNV deletion 23290073
esv2738080 CNV deletion 23290073
esv2738082 CNV deletion 23290073
esv2738083 CNV deletion 23290073
esv2738086 CNV deletion 23290073
esv2738088 CNV deletion 23290073
esv28359 CNV loss 19812545
esv3333453 CNV duplication 20981092
esv3576611 CNV gain 25503493
esv3619132 CNV loss 21293372
nsv1077528 CNV duplication 25765185
nsv1128461 CNV deletion 24896259
nsv428208 CNV gain 18775914
nsv522459 CNV loss 19592680
nsv612940 CNV loss 21841781
nsv612951 CNV loss 21841781
nsv831489 CNV loss 17160897
nsv831490 CNV loss 17160897
nsv950824 CNV deletion 24416366
nsv958500 CNV deletion 24416366

Variation tolerance for ARHGAP39 Gene

Residual Variation Intolerance Score: 6.25% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.07; 50.69% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ARHGAP39 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ARHGAP39 Gene

Disorders for ARHGAP39 Gene

MalaCards: The human disease database

(4) MalaCards diseases for ARHGAP39 Gene - From: DISEASES

- elite association - COSMIC cancer census association via MalaCards
genes like me logo Genes that share disorders with ARHGAP39: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ARHGAP39 Gene

Publications for ARHGAP39 Gene

  1. Cross GTPase-activating protein (CrossGAP)/Vilse links the Roundabout receptor to Rac to regulate midline repulsion. (PMID: 15755809) Hu H … Bashaw GJ (Proceedings of the National Academy of Sciences of the United States of America 2005) 2 3
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  3. 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. (PMID: 11214970) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 3 4
  4. PLEKHA4/kramer Attenuates Dishevelled Ubiquitination to Modulate Wnt and Planar Cell Polarity Signaling. (PMID: 31091453) Shami Shah A … Baskin JM (Cell reports 2019) 3
  5. VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. (PMID: 29507755) Yue Y … Liu J (Cell discovery 2018) 3

Products for ARHGAP39 Gene

Sources for ARHGAP39 Gene