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

Summary

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: mouse all
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Genomic context

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_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
[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].
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.
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.
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.
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.
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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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
A genome-wide association study identifies a potential novel gene locus for keratoconus, one of the commonest causes for corneal transplantation in developed countries. EBI GWAS Catalog EBI GWAS CatalogPubMed
An atlas of genetic influences on human blood metabolites. EBI GWAS Catalog EBI GWAS CatalogPubMed
Biological, clinical and population relevance of 95 loci for blood lipids. EBI GWAS Catalog EBI GWAS CatalogPubMed
Discovery and refinement of loci associated with lipid levels. 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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Markers

D2S2871 (e-PCR)
- UniSTS:11276

SGC32369 (e-PCR)
- UniSTS:66317

SHGC-31260 (e-PCR)
- UniSTS:31772

G16390 (e-PCR)
- UniSTS:5936

RH67847 (e-PCR)
- UniSTS:49267

WI-17012 (e-PCR)
- UniSTS:28796

RH25298 (e-PCR)
- UniSTS:70530

A008U03 (e-PCR)
- UniSTS:82818

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 more info	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

NG_016972.2 RefSeqGene

Range

5002..123420

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

135052292..135176396

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

RNA

XR_001738674.3 RNA Sequence

Related

ENST00000487003.5

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

135492756..135617244

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A8J9AUI2
XM_054341045.1 → XP_054197020.1 rab3 GTPase-activating protein catalytic subunit isoform X2
XM_054341046.1 → XP_054197021.1 rab3 GTPase-activating protein catalytic subunit isoform X3