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

Gene ID: 22930, updated on 3-Nov-2024

Summary

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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; AllianceGenome:HGNC:17063
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; MARTS2; 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
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Genomic context

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See RAB3GAP1 in Genome Data Viewer
Location:
2q21.3
Exon count:
29
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (135052292..135176396)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (135492756..135617244)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (135809862..135928280)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16568 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16569 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11980 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:135732781-135733282 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:135733283-135733782 Neighboring gene cyclin T2 Neighboring gene mitogen-activated protein kinase kinase kinase 19 Neighboring gene MPRA-validated peak3873 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16570 Neighboring gene small nucleolar RNA U13 Neighboring gene HNF4 motif-containing MPRA enhancer 203 Neighboring gene small nucleolar RNA, H/ACA box 40B Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:135970274-135970798 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:135980911-135981075 Neighboring gene uncharacterized LOC124906077 Neighboring gene zinc finger RANBP2-type containing 3 Neighboring gene MPRA-validated peak3875 silencer Neighboring gene G3BP1 pseudogene 1

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 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. Proteasomal degradation of p130 facilitate cell cycle deregulation and impairment of cellular differentiation in high-risk Human Papillomavirus 16 and 18 E7 transfected cells. Gandhi S, et al. Mol Biol Rep, 2021 Jun. PMID 34169395
  2. Revealing the functions of novel mutations in RAB3GAP1 in Martsolf and Warburg micro syndromes. Koparir A, et al. Am J Med Genet A, 2019 Apr. PMID 30730599
  3. Novel RAB3GAP1 compound heterozygous mutations in Japanese siblings with Warburg Micro syndrome. Asahina M, et al. Brain Dev, 2016 Mar. PMID 26421802
  4. Consanguinity as an Adjunct Diagnostic Tool. Srivastava P, et al. Indian J Pediatr, 2016 Mar. PMID 26138576
  5. Large homozygous RAB3GAP1 gene microdeletion causes Warburg micro syndrome 1. Picker-Minh S, et al. Orphanet J Rare Dis, 2014 Oct 21. PMID 25332050, Free PMC Article

See all (114) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Exome sequencing identifies a novel pathogenic variant in RAB3GAP1 causing Warburg Micro syndrome in a Pakistani family.
    Title: Exome sequencing identifies a novel pathogenic variant in RAB3GAP1 causing Warburg Micro syndrome in a Pakistani family.
  2. Proteasomal degradation of p130 facilitate cell cycle deregulation and impairment of cellular differentiation in high-risk Human Papillomavirus 16 and 18 E7 transfected cells.
    Title: Proteasomal degradation of p130 facilitate cell cycle deregulation and impairment of cellular differentiation in high-risk Human Papillomavirus 16 and 18 E7 transfected cells.
  3. Micro and Martsolf syndromes in 34 new patients: Refining the phenotypic spectrum and further molecular insights.
    Title: Micro and Martsolf syndromes in 34 new patients: Refining the phenotypic spectrum and further molecular insights.
  4. Novel manifestations of Warburg micro syndrome type 1 caused by a new splicing variant of RAB3GAP1: a case report.
    Title: Novel manifestations of Warburg micro syndrome type 1 caused by a new splicing variant of RAB3GAP1: a case report.
  5. [Analysis of a case of Warburg micro syndrome type 1 due to variant of RAB3GAP1 gene].
    Title: [Analysis of a case of Warburg micro syndrome type 1 due to variant of RAB3GAP1 gene].
  6. Mutations in RAB3GAP1 gene are associated with Martsolf and Warburg micro syndromes.
    Title: Revealing the functions of novel mutations in RAB3GAP1 in Martsolf and Warburg micro syndromes.
  7. overexpressing p130 or E2F4 significantly improved migration but not proliferation of mMSCs. Our data suggest that cell cycle regulation may be involved in p130/E2F4-mediated changes in the multipotential abilities of bone-marrow-derived mesenchymal stem cells (MSCs).
    Title: Stable overexpression of p130/E2F4 affects the multipotential abilities of bone-marrow-derived mesenchymal stem cells.
  8. Whole-exome sequencing, using DNA of the first fetus, was performed shortly after the birth of a male child, and two truncating RAB3GAP1 mutations were detected: c.538G>T; p. (Glu180*) and c.943C>T; p. (Arg315*).
    Title: Early detection of bilateral cataracts in utero may represent a manifestation of severe congenital disease.
  9. show that FOXC1 regulates the expression of RAB3GAP1, RAB3GAP2 and SNAP25
    Title: FOXC1 modulates MYOC secretion through regulation of the exocytic proteins RAB3GAP1, RAB3GAP2 and SNAP25.
  10. RAB18 modulates macroautophagy and proteostasis, and is dependent on activity of RAB3GAP1 and RAB3GAP2.
    Title: The RAB GTPase RAB18 modulates macroautophagy and proteostasis.
Submit: New GeneRIF Correction See all GeneRIFs (26)

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

Associated conditions

Description Tests
Martsolf syndrome 2
MedGen: C5543626 OMIM: 619420 GeneReviews: Not available
Compare labs
Warburg micro syndrome 1
MedGen: C1838625 OMIM: 600118 GeneReviews: RAB18 Deficiency
Compare labs

EBI GWAS Catalog

Description
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EBI GWAS Catalog
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Discovery and refinement of loci associated with lipid levels.
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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Markers

Homology

Clone Names

  • KIAA0066, DKFZp434A012

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 IDA
Inferred from Direct Assay
more info
 PubMed 
enables GTPase activator activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
contributes_to guanyl-nucleotide exchange factor activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables guanyl-nucleotide exchange factor activity TAS
Traceable Author Statement
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables small GTPase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in brain development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in brain development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in camera-type eye development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in establishment of protein localization to endoplasmic reticulum membrane IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in excitatory postsynaptic potential ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in face morphogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in hypothalamus development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within lipid droplet organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of GTPase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of GTPase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of autophagosome assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of autophagosome assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of endoplasmic reticulum tubular network organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of glutamate neurotransmitter secretion in response to membrane depolarization ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of protein lipidation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of GTPase activity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of calcium ion-dependent exocytosis of neurotransmitter ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of short-term neuronal synaptic plasticity ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  
located_in endoplasmic reticulum tubular network IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular exosome HDA PubMed 
located_in lipid droplet IDA
Inferred from Direct Assay
more info
 PubMed 
located_in postsynapse IEA
Inferred from Electronic Annotation
more info
  
part_of protein-containing complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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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

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.

Genomic

  1. NG_016972.2 RefSeqGene

    Range
    5002..123420
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001172435.2 → NP_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
    Related
    ENSP00000411418.1, ENST00000442034.5
    Conserved Domains (2) summary
    pfam13890
    Location:612 → 769
    Rab3-GTPase_cat; Rab3 GTPase-activating protein catalytic subunit
    pfam15810
    Location:881 → 970
    CCDC117; Coiled-coil domain-containing protein 117

  2. NM_012233.3 → NP_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
    A6H8Z3, C9J837, Q15042, Q659F5, Q8TBB4
    UniProtKB/TrEMBL
    B9A6J2
    Related
    ENSP00000264158.8, ENST00000264158.13
    Conserved Domains (1) summary
    pfam13890
    Location:612 → 769
    Rab3-GTPase_cat; Rab3 GTPase-activating protein catalytic subunit

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    135052292..135176396
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011510823.4 → XP_011509125.1  rab3 GTPase-activating protein catalytic subunit isoform X1

    UniProtKB/TrEMBL
    A0A8J9AUI2
    Related
    ENSP00000444306.2, ENST00000539493.3
    Conserved Domains (1) summary
    pfam13890
    Location:612 → 769
    Rab3-GTPase_cat; Rab3 GTPase-activating protein catalytic subunit

  2. XM_011510825.4 → XP_011509127.1  rab3 GTPase-activating protein catalytic subunit isoform X2

    Conserved Domains (1) summary
    pfam13890
    Location:612 → 769
    Rab3-GTPase_cat; Rab3 GTPase-activating protein catalytic subunit

  3. XM_047443732.1 → XP_047299688.1  rab3 GTPase-activating protein catalytic subunit isoform X3

RNA

  1. XR_001738674.3 RNA Sequence

    Related
    ENST00000487003.5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    135492756..135617244
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054341044.1 → XP_054197019.1  rab3 GTPase-activating protein catalytic subunit isoform X1

    UniProtKB/TrEMBL
    A0A8J9AUI2

  2. XM_054341045.1 → XP_054197020.1  rab3 GTPase-activating protein catalytic subunit isoform X2

  3. XM_054341046.1 → XP_054197021.1  rab3 GTPase-activating protein catalytic subunit isoform X3

RNA

  1. XR_008486307.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q15042.3 GenPept UniProtKB/Swiss-Prot:Q15042

Gene LinkOut

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