Free for academic non-profit institutions. Other users need a Commercial license

Aliases for RAB3GAP1 Gene

Aliases for RAB3GAP1 Gene

  • RAB3 GTPase Activating Protein Catalytic Subunit 1 2 3 5
  • RAB3 GTPase Activating Protein Subunit 1 (Catalytic) 2 3
  • RAB3 GTPase-Activating Protein 130 KDa Subunit 3 4
  • Rab3-GAP P130 3 4
  • RAB3GAP 3 4
  • Rab3 GTPase-Activating Protein Catalytic Subunit 3
  • RAB3GAP130 3
  • KIAA0066 4
  • Rab3-GAP 4
  • WARBM1 3
  • P130 3

External Ids for RAB3GAP1 Gene

Previous GeneCards Identifiers for RAB3GAP1 Gene

  • GC02P135645
  • GC02U900802
  • GC02P135526
  • GC02P135809
  • GC02P127801

Summaries for RAB3GAP1 Gene

Entrez Gene Summary for RAB3GAP1 Gene

  • 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]

GeneCards Summary for RAB3GAP1 Gene

RAB3GAP1 (RAB3 GTPase Activating Protein Catalytic Subunit 1) is a Protein Coding gene. Diseases associated with RAB3GAP1 include Warburg Micro Syndrome 1 and Martsolf Syndrome. Among its related pathways are COPI-independent Golgi-to-ER retrograde traffic and Golgi-to-ER retrograde transport. Gene Ontology (GO) annotations related to this gene include GTPase activator activity and Rab guanyl-nucleotide exchange factor activity.

UniProtKB/Swiss-Prot for RAB3GAP1 Gene

  • Probable catalytic subunit of a GTPase activating protein that has specificity for Rab3 subfamily (RAB3A, RAB3B, RAB3C and RAB3D). Rab3 proteins are involved in regulated exocytosis of neurotransmitters and hormones. Specifically converts active Rab3-GTP to the inactive form Rab3-GDP. Required for normal eye and brain development. May participate in neurodevelopmental processes such as proliferation, migration and differentiation before synapse formation, and non-synaptic vesicular release of neurotransmitters.

Gene Wiki entry for RAB3GAP1 Gene

Additional gene information for RAB3GAP1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RAB3GAP1 Gene

Genomics for RAB3GAP1 Gene

GeneHancer (GH) Regulatory Elements for RAB3GAP1 Gene

Promoters and enhancers for RAB3GAP1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02I135051 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 550.8 +1.3 1331 3.8 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 RAB3GAP1 MAP3K19 CCNT2 UBXN4 DARS ZRANB3 GC02P135138
GH02I135050 Enhancer 0.7 ENCODE 550.8 -1.3 -1321 0.5 ATF1 PKNOX1 NFATC3 SOX6 TEAD4 TAL1 CBFA2T3 HMG20A DPF2 EP300 RAB3GAP1 MAP3K19
GH02I135797 Enhancer 1 Ensembl ENCODE 9.6 +745.4 745435 0.6 PKNOX1 CLOCK ATF1 RB1 ARID4B SIN3A RAD21 EGR1 ZNF143 RUNX3 LOC100507600 LCT MCM6 MAP3K19 RAB3GAP1 DARS GC02M135811 GC02M135782 ENSG00000200664 GC02M135791
GH02I135980 Enhancer 0.9 ENCODE dbSUPER 10 +928.7 928661 0.7 PKNOX1 BMI1 ATF7 RUNX3 IKZF2 ZNF687 NR2F1 TRIM22 DPF2 BRF2 RAB3GAP1 DARS DARS-AS1 GC02P135903
GH02I135149 Enhancer 0.8 ENCODE 11 +99.2 99221 3 CLOCK FOXA2 ARID4B YBX1 ZSCAN9 RARA FOS THAP11 RXRA SP5 MAP3K19 RAB3GAP1 GC02M135137 PIR52405 ZRANB3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RAB3GAP1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RAB3GAP1 gene promoter:

Genomic Locations for RAB3GAP1 Gene

Genomic Locations for RAB3GAP1 Gene
chr2:135,052,265-135,176,394
(GRCh38/hg38)
Size:
124,130 bases
Orientation:
Plus strand
chr2:135,809,835-135,933,964
(GRCh37/hg19)

Genomic View for RAB3GAP1 Gene

Genes around RAB3GAP1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RAB3GAP1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RAB3GAP1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RAB3GAP1 Gene

Proteins for RAB3GAP1 Gene

  • Protein details for RAB3GAP1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q15042-RB3GP_HUMAN
    Recommended name:
    Rab3 GTPase-activating protein catalytic subunit
    Protein Accession:
    Q15042
    Secondary Accessions:
    • A6H8Z3
    • C9J837
    • Q659F5
    • Q8TBB4

    Protein attributes for RAB3GAP1 Gene

    Size:
    981 amino acids
    Molecular mass:
    110524 Da
    Quaternary structure:
    • The Rab3 GTPase-activating complex is a heterodimer composed of RAB3GAP and RAB3-GAP150. The Rab3 GTPase-activating complex interacts with DMXL2 (By similarity). Interacts with LMAN1 (PubMed:22337587).
    SequenceCaution:
    • Sequence=BC071602; Type=Frameshift; Positions=211; Evidence={ECO:0000305}; Sequence=CAH56411.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact.; Evidence={ECO:0000305};

    Alternative splice isoforms for RAB3GAP1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RAB3GAP1 Gene

Post-translational modifications for RAB3GAP1 Gene

  • Ubiquitination at Lys38, isoforms=346, isoforms=350, Lys197, Lys316, Lys338, Lys896, and isoforms=3, 4965

Other Protein References for RAB3GAP1 Gene

No data available for DME Specific Peptides for RAB3GAP1 Gene

Domains & Families for RAB3GAP1 Gene

Gene Families for RAB3GAP1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for RAB3GAP1 Gene

InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

Q15042

UniProtKB/Swiss-Prot:

RB3GP_HUMAN :
  • Belongs to the Rab3-GAP catalytic subunit family.
Family:
  • Belongs to the Rab3-GAP catalytic subunit family.
genes like me logo Genes that share domains with RAB3GAP1: view

Function for RAB3GAP1 Gene

Molecular function for RAB3GAP1 Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=75 uM for GTP-loaded RAB3A {ECO:0000269 PubMed:10859313};
UniProtKB/Swiss-Prot Function:
Probable catalytic subunit of a GTPase activating protein that has specificity for Rab3 subfamily (RAB3A, RAB3B, RAB3C and RAB3D). Rab3 proteins are involved in regulated exocytosis of neurotransmitters and hormones. Specifically converts active Rab3-GTP to the inactive form Rab3-GDP. Required for normal eye and brain development. May participate in neurodevelopmental processes such as proliferation, migration and differentiation before synapse formation, and non-synaptic vesicular release of neurotransmitters.

Phenotypes From GWAS Catalog for RAB3GAP1 Gene

Gene Ontology (GO) - Molecular Function for RAB3GAP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005085 guanyl-nucleotide exchange factor activity TAS --
GO:0005096 GTPase activator activity IMP 24891604
GO:0005515 protein binding IPI 22337587
GO:0017112 contributes_to Rab guanyl-nucleotide exchange factor activity IMP 24891604
GO:0017137 Rab GTPase binding IPI 10859313
genes like me logo Genes that share ontologies with RAB3GAP1: view

Phenotypes for RAB3GAP1 Gene

genes like me logo Genes that share phenotypes with RAB3GAP1: view

Human Phenotype Ontology for RAB3GAP1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for RAB3GAP1 Gene

MGI Knock Outs for RAB3GAP1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for RAB3GAP1 Gene

Localization for RAB3GAP1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RAB3GAP1 Gene

Cytoplasm. Note=In neurons, it is enriched in the synaptic soluble fraction.

Subcellular locations from

COMPARTMENTS
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 RAB3GAP1 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 5
cytosol 5
golgi apparatus 4
nucleus 2

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for RAB3GAP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0005794 Golgi apparatus IDA 25495476
GO:0005811 lipid droplet IDA 25495476
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with RAB3GAP1: view

Pathways & Interactions for RAB3GAP1 Gene

genes like me logo Genes that share pathways with RAB3GAP1: view

Gene Ontology (GO) - Biological Process for RAB3GAP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007420 brain development IMP 20512159
GO:0010628 positive regulation of gene expression IEA --
GO:0021854 hypothalamus development IMP 20512159
GO:0034389 lipid particle organization IMP 24239381
GO:0043010 camera-type eye development IMP 20512159
genes like me logo Genes that share ontologies with RAB3GAP1: view

No data available for SIGNOR curated interactions for RAB3GAP1 Gene

Drugs & Compounds for RAB3GAP1 Gene

(1) Drugs for RAB3GAP1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Guanosine triphosphate Experimental Pharma 0

(2) Additional Compounds for RAB3GAP1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with RAB3GAP1: view

Transcripts for RAB3GAP1 Gene

mRNA/cDNA for RAB3GAP1 Gene

(4) REFSEQ mRNAs :
(9) Additional mRNA sequences :
(7) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for RAB3GAP1 Gene

RAB3 GTPase activating protein subunit 1 (catalytic):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RAB3GAP1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b · 8c ^ 9a · 9b ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13 ^ 14a · 14b ^ 15a · 15b ^ 16
SP1:
SP2: -
SP3:
SP4:
SP5: -
SP6:
SP7:
SP8:

Relevant External Links for RAB3GAP1 Gene

GeneLoc Exon Structure for
RAB3GAP1
ECgene alternative splicing isoforms for
RAB3GAP1

Expression for RAB3GAP1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RAB3GAP1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RAB3GAP1 Gene

This gene is overexpressed in Heart (20.2) and Peripheral blood mononuclear cells (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RAB3GAP1 Gene



Protein tissue co-expression partners for RAB3GAP1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RAB3GAP1 Gene:

RAB3GAP1

SOURCE GeneReport for Unigene cluster for RAB3GAP1 Gene:

Hs.306327

mRNA Expression by UniProt/SwissProt for RAB3GAP1 Gene:

Q15042-RB3GP_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for RAB3GAP1 Gene

  • Liver(4.3)
  • Nervous system(4.3)
  • Bone marrow(4.2)
  • Adrenal gland(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for RAB3GAP1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • outer ear
  • pituitary gland
  • scalp
  • skull
  • tongue
  • tooth
Thorax:
  • breast
  • chest wall
  • clavicle
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
  • trachea
Abdomen:
  • abdominal wall
Pelvis:
  • ovary
  • pelvis
  • penis
  • prostate
  • testicle
  • uterus
  • vagina
  • vulva
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • nail
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood vessel
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with RAB3GAP1: view

Primer Products

No data available for mRNA differential expression in normal tissues for RAB3GAP1 Gene

Orthologs for RAB3GAP1 Gene

This gene was present in the common ancestor of animals.

Orthologs for RAB3GAP1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RAB3GAP1 33 34
  • 99.63 (n)
dog
(Canis familiaris)
Mammalia RAB3GAP1 33 34
  • 92.86 (n)
cow
(Bos Taurus)
Mammalia RAB3GAP1 33 34
  • 91.95 (n)
oppossum
(Monodelphis domestica)
Mammalia RAB3GAP1 34
  • 88 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Rab3gap1 33 16 34
  • 87.11 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RAB3GAP1 34
  • 80 (a)
OneToOne
chicken
(Gallus gallus)
Aves RAB3GAP1 33 34
  • 80.26 (n)
lizard
(Anolis carolinensis)
Reptilia RAB3GAP1 34
  • 86 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rab3gap1 33
  • 72.39 (n)
zebrafish
(Danio rerio)
Actinopterygii rab3gap1 33 34
  • 66.8 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG31935 33 34
  • 46.76 (n)
worm
(Caenorhabditis elegans)
Secernentea rbg-1 33 34
  • 44.86 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 39 (a)
OneToOne
Species where no ortholog for RAB3GAP1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • rat (Rattus norvegicus)
  • 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)
  • wheat (Triticum aestivum)

Evolution for RAB3GAP1 Gene

ENSEMBL:
Gene Tree for RAB3GAP1 (if available)
TreeFam:
Gene Tree for RAB3GAP1 (if available)

Paralogs for RAB3GAP1 Gene

No data available for Paralogs for RAB3GAP1 Gene

Variants for RAB3GAP1 Gene

Sequence variations from dbSNP and Humsavar for RAB3GAP1 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs10170125 likely-benign, Warburg micro syndrome 135,168,916(+) C/G 3_prime_UTR_variant, intron_variant
rs10445686 conflicting-interpretations-of-pathogenicity, benign, not specified, Warburg micro syndrome 135,135,802(+) A/C/G coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs1050515610 uncertain-significance, Warburg micro syndrome 135,169,105(+) T/G 3_prime_UTR_variant, intron_variant
rs1064794536 pathogenic, not provided, Warburg micro syndrome 1 135,115,364(+) /C coding_sequence_variant, frameshift, non_coding_transcript_variant
rs114901298 likely-benign, not specified, Warburg micro syndrome 135,132,983(+) A/G coding_sequence_variant, missense_variant, non_coding_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for RAB3GAP1 Gene

Variant ID Type Subtype PubMed ID
nsv979128 CNV duplication 23825009
nsv834386 CNV gain 17160897
nsv583171 CNV loss 21841781
esv3592571 CNV loss 21293372
esv3592568 CNV loss 21293372

Variation tolerance for RAB3GAP1 Gene

Residual Variation Intolerance Score: 14% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.86; 86.99% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RAB3GAP1 Gene

Human Gene Mutation Database (HGMD)
RAB3GAP1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RAB3GAP1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RAB3GAP1 Gene

Disorders for RAB3GAP1 Gene

MalaCards: The human disease database

(11) MalaCards diseases for RAB3GAP1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
warburg micro syndrome 1
  • warbm1
martsolf syndrome
  • cataract-mental retardation-hypogonadism
warburg micro syndrome
  • micro syndrome
spastic diplegia
  • cerebral spastic infantile paralysis
rab18 deficiency
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

RB3GP_HUMAN
  • Warburg micro syndrome 1 (WARBM1) [MIM:600118]: A rare syndrome characterized by microcephaly, microphthalmia, microcornia, congenital cataracts, optic atrophy, cortical dysplasia, in particular corpus callosum hypoplasia, severe mental retardation, spastic diplegia, and hypogonadism. {ECO:0000269 PubMed:15696165}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for RAB3GAP1

genes like me logo Genes that share disorders with RAB3GAP1: view

No data available for Genatlas for RAB3GAP1 Gene

Publications for RAB3GAP1 Gene

  1. Mutations of the catalytic subunit of RAB3GAP cause Warburg Micro syndrome. (PMID: 15696165) Aligianis IA … Maher ER (Nature genetics 2005) 2 3 4 22 58
  2. Isolation and characterization of a GTPase activating protein specific for the Rab3 subfamily of small G proteins. (PMID: 9030515) Fukui K … Takai Y (The Journal of biological chemistry 1997) 2 3 4 22 58
  3. Biochemical characterization of Rab3-GTPase-activating protein reveals a mechanism similar to that of Ras-GAP. (PMID: 10859313) Clabecq A … Darchen F (The Journal of biological chemistry 2000) 3 4 22 58
  4. Localization of the Rab3 small G protein regulators in nerve terminals and their involvement in Ca2+-dependent exocytosis. (PMID: 9852129) Oishi H … Takai Y (The Journal of biological chemistry 1998) 3 4 22 58
  5. Protein interaction profiling of the p97 adaptor UBXD1 points to a role for the complex in modulating ERGIC-53 trafficking. (PMID: 22337587) Haines DS … Deshaies RJ (Molecular & cellular proteomics : MCP 2012) 3 4 58

Products for RAB3GAP1 Gene

Sources for RAB3GAP1 Gene

Content
Loading form....