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

Summary

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, Nov 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

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_000008.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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 EBI GWAS CatalogPubMed
Genome-wide association study of smoking behaviours among Bangladeshi adults. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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)

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
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
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

NC_000008.11 Reference GRCh38.p14 Primary Assembly

Range

144529179..144700362 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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