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RAB3GAP1 RAB3 GTPase activating protein catalytic subunit 1 [ Homo sapiens (human) ]

Gene ID: 22930, updated on 3-Jun-2018
Official Symbol
RAB3GAP1provided by HGNC
Official Full Name
RAB3 GTPase activating protein catalytic subunit 1provided by HGNC
Primary source
HGNC:HGNC:17063
See related
Ensembl:ENSG00000115839 MIM:602536; Vega:OTTHUMG00000154889
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
P130; WARBM1; RAB3GAP; RAB3GAP130
Summary
This gene encodes the catalytic subunit of a Rab GTPase activating protein. The encoded protein forms a heterodimer with a non-catalytic subunit to specifically regulate the activity of members of the Rab3 subfamily of small G proteins. This protein mediates the hydrolysis of GTP bound Rab3 to the GDP bound form. Mutations in this gene are associated with Warburg micro syndrome. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Feb 2010]
Expression
Ubiquitous expression in brain (RPKM 16.8), thyroid (RPKM 15.9) and 25 other tissues See more
Orthologs
See RAB3GAP1 in Genome Data Viewer
Location:
2q21.3
Exon count:
27
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (135052265..135176667)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (135809835..135928280)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene cyclin T2 Neighboring gene mitogen-activated protein kinase kinase kinase 19 Neighboring gene HNF4 motif-containing MPRA enhancer 203 Neighboring gene small nucleolar RNA, H/ACA box 40B Neighboring gene zinc finger RANBP2-type containing 3 Neighboring gene G3BP stress granule assembly factor 1 pseudogene Neighboring gene R3H domain containing 1 Neighboring gene RNA, U6 small nuclear 512, pseudogene

  • 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Warburg micro syndrome 1
MedGen: C1838625 OMIM: 600118 GeneReviews: RAB18 Deficiency
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NHGRI GWAS Catalog

Description
A genome-wide association study identifies a potential novel gene locus for keratoconus, one of the commonest causes for corneal transplantation in developed countries.
NHGRI GWA Catalog
An atlas of genetic influences on human blood metabolites.
NHGRI GWA Catalog
Biological, clinical and population relevance of 95 loci for blood lipids.
NHGRI GWA Catalog
Discovery and refinement of loci associated with lipid levels.
NHGRI GWA Catalog
  • COPI-independent Golgi-to-ER retrograde traffic, organism-specific biosystem (from REACTOME)
    COPI-independent Golgi-to-ER retrograde traffic, organism-specific biosystemIn addition to the better characterized COPI-dependent retrograde Golgi-to-ER pathway, a second COPI-independent pathway has also been identified. This pathway is RAB6 dependent and transports cargo...
  • Golgi-to-ER retrograde transport, organism-specific biosystem (from REACTOME)
    Golgi-to-ER retrograde transport, organism-specific biosystemRetrograde traffic from the cis-Golgi to the ERGIC or the ER occurs through either COPI-coated vesicles or through a less well characterized RAB6-dependent route that makes use of tubular carriers (r...
  • Intra-Golgi and retrograde Golgi-to-ER traffic, organism-specific biosystem (from REACTOME)
    Intra-Golgi and retrograde Golgi-to-ER traffic, organism-specific biosystemThe mammalian Golgi complex, a central hub of both anterograde and retrograde trafficking, is a ribbon of stacked cisterna with biochemically distinct compartments (reviewed in Glick and Nakano, 2009...
  • Membrane Trafficking, organism-specific biosystem (from REACTOME)
    Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
  • RAB GEFs exchange GTP for GDP on RABs, organism-specific biosystem (from REACTOME)
    RAB GEFs exchange GTP for GDP on RABs, organism-specific biosystemHuman cells have more than 60 RAB proteins that are key regulators of intracellular membrane trafficking. These small GTPases contribute to trafficking specificity by localizing to the membranes of d...
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • KIAA0066, DKFZp434A012

Gene Ontology Provided by GOA

Function Evidence Code Pubs
GTPase activator activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
GTPase activator activity IDA
Inferred from Direct Assay
more info
PubMed 
GTPase activator activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
Rab GTPase binding IPI
Inferred from Physical Interaction
more info
PubMed 
contributes_to Rab guanyl-nucleotide exchange factor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
guanyl-nucleotide exchange factor activity TAS
Traceable Author Statement
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
brain development IMP
Inferred from Mutant Phenotype
more info
PubMed 
camera-type eye development IMP
Inferred from Mutant Phenotype
more info
PubMed 
establishment of protein localization to endoplasmic reticulum membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 
excitatory postsynaptic potential ISS
Inferred from Sequence or Structural Similarity
more info
 
face morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
hypothalamus development IMP
Inferred from Mutant Phenotype
more info
PubMed 
lipid particle organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of GTPase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of GTPase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of autophagosome assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of endoplasmic reticulum tubular network organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of gene expression IEA
Inferred from Electronic Annotation
more info
 
positive regulation of glutamate neurotransmitter secretion in response to membrane depolarization ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of protein lipidation IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of GTPase activity IDA
Inferred from Direct Assay
more info
PubMed 
regulation of calcium ion-dependent exocytosis of neurotransmitter ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of short-term neuronal synaptic plasticity ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 
endoplasmic reticulum tubular network IDA
Inferred from Direct Assay
more info
PubMed 
extracellular exosome HDA PubMed 
lipid droplet IDA
Inferred from Direct Assay
more info
PubMed 
postsynapse IEA
Inferred from Electronic Annotation
more info
 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
rab3 GTPase-activating protein catalytic subunit
Names
RAB3 GTPase activating protein subunit 1 (catalytic)
RAB3 GTPase-activating protein 130 kDa subunit
rab3-GAP p130

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.

Genomic

  1. NG_016972.1 RefSeqGene

    Range
    5001..123446
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001172435.1NP_001165906.1  rab3 GTPase-activating protein catalytic subunit isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC017031, BC071602, DA333844
    Consensus CDS
    CCDS54402.1
    UniProtKB/Swiss-Prot
    Q15042
    Related
    ENSP00000411418.1, OTTHUMP00000206879, ENST00000442034.5, OTTHUMT00000337515
    Conserved Domains (2) summary
    pfam13890
    Location:612769
    Rab3-GTPase_cat; Rab3 GTPase-activating protein catalytic subunit
    pfam15810
    Location:881970
    CCDC117; Coiled-coil domain-containing protein 117
  2. NM_012233.2NP_036365.1  rab3 GTPase-activating protein catalytic subunit isoform 2

    See identical proteins and their annotated locations for NP_036365.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC017031, D31886, DA333844
    Consensus CDS
    CCDS33294.1
    UniProtKB/Swiss-Prot
    Q15042
    UniProtKB/TrEMBL
    B9A6J2
    Related
    ENSP00000264158.7, OTTHUMP00000206878, ENST00000264158.12, OTTHUMT00000337514
    Conserved Domains (1) summary
    pfam13890
    Location:612769
    Rab3-GTPase_cat; Rab3 GTPase-activating protein catalytic subunit

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

    Range
    135052265..135176667
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011510823.3XP_011509125.1  rab3 GTPase-activating protein catalytic subunit isoform X1

    Related
    ENSP00000444306.1, ENST00000539493.2
    Conserved Domains (1) summary
    pfam13890
    Location:612769
    Rab3-GTPase_cat; Rab3 GTPase-activating protein catalytic subunit
  2. XM_011510825.3XP_011509127.1  rab3 GTPase-activating protein catalytic subunit isoform X2

    Conserved Domains (1) summary
    pfam13890
    Location:612769
    Rab3-GTPase_cat; Rab3 GTPase-activating protein catalytic subunit

RNA

  1. XR_001738674.2 RNA Sequence

    Related
    ENST00000487003.5
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