Human Gene RAB3GAP2 (uc010puk.1) Description and Page Index
  Description: Homo sapiens RAB3 GTPase activating protein subunit 2 (non-catalytic) (RAB3GAP2), mRNA.
RefSeq Summary (NM_012414): The protein encoded by this gene belongs to the RAB3 protein family, members of which are involved in regulated exocytosis of neurotransmitters and hormones. This protein forms the Rab3 GTPase-activating complex with RAB3GAP1, where it constitutes the regulatory subunit, whereas the latter functions as the catalytic subunit. This gene has the highest level of expression in the brain, consistent with it having a key role in neurodevelopment. Mutations in this gene are associated with Martsolf syndrome.[provided by RefSeq, Oct 2009]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR1660809.233194.1, SRR1660807.139839.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000358951.7/ ENSP00000351832.2 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr1:220,321,610-220,445,843 Size: 124,234 Total Exon Count: 35 Strand: -
Coding Region
   Position: hg19 chr1:220,324,593-220,445,679 Size: 121,087 Coding Exon Count: 35 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:220,321,610-220,445,843)mRNA (may differ from genome)Protein (1393 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: RBGPR_HUMAN
DESCRIPTION: RecName: Full=Rab3 GTPase-activating protein non-catalytic subunit; AltName: Full=RGAP-iso; AltName: Full=Rab3 GTPase-activating protein 150 kDa subunit; AltName: Full=Rab3-GAP p150; Short=Rab3-GAP150; AltName: Full=Rab3-GAP regulatory subunit;
FUNCTION: Regulatory 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. Rab3 GTPase-activating complex 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.
SUBUNIT: The Rab3 GTPase-activating complex is a heterodimer composed of RAB3GAP and RAB3-GAP150. The Rab3 GTPase-activating complex interacts with DMXL2 (By similarity).
INTERACTION: O75365:PTP4A3; NbExp=1; IntAct=EBI-536107, EBI-1043866;
SUBCELLULAR LOCATION: Cytoplasm. Note=In neurons, it is enriched in the synaptic soluble fraction.
TISSUE SPECIFICITY: Ubiquitous.
DISEASE: Defects in RAB3GAP2 are the cause of Martsolf syndrome (MARTS) [MIM:212720]. Martsolf syndrome is characterized by congenital cataracts, mental retardation, and hypogonadism. Inheritance is autosomal recessive.
DISEASE: Defects in RAB3GAP2 are the cause of Warburg micro syndrome type 2 (WARBM2) [MIM:614225]. WARBM2 is 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.
SIMILARITY: Belongs to the Rab3-GAP regulatory subunit family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RAB3GAP2
CDC HuGE Published Literature: RAB3GAP2
Positive Disease Associations: Abdominal Fat , Body Mass Index , Body Weight , C-Reactive Protein , Cholesterol, HDL
Related Studies:
  1. Abdominal Fat
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.
  2. Body Mass Index
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.
  3. Body Weight
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: RAB3GAP2
Diseases sorted by gene-association score: martsolf syndrome* (1699), warburg micro syndrome 2* (1019), autosomal recessive spastic paraplegia type 69* (350), warburg micro syndrome (19), warburg micro syndrome 4 (12), steroid-induced glaucoma (11), warburg micro syndrome 1 (11), spastic diplegia (7), axenfeld-rieger syndrome (4)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 12.21 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 200.84 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -68.80164-0.420 Picture PostScript Text
3' UTR -711.122983-0.238 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR026059 - Rab3-gap_reg

Pfam Domains:
PF14655 - Rab3 GTPase-activating protein regulatory subunit N-terminus
PF14656 - Rab3 GTPase-activating protein regulatory subunit C-terminus

ModBase Predicted Comparative 3D Structure on Q9H2M9
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005096 GTPase activator activity
GO:0005515 protein binding
GO:0008047 enzyme activator activity
GO:0017137 Rab GTPase binding
GO:0030234 enzyme regulator activity
GO:0046982 protein heterodimerization activity
GO:0017112 Rab guanyl-nucleotide exchange factor activity

Biological Process:
GO:0006886 intracellular protein transport
GO:0043085 positive regulation of catalytic activity
GO:0043087 regulation of GTPase activity
GO:0043547 positive regulation of GTPase activity
GO:0097051 establishment of protein localization to endoplasmic reticulum membrane
GO:1903061 positive regulation of protein lipidation
GO:1903373 positive regulation of endoplasmic reticulum tubular network organization
GO:2000786 positive regulation of autophagosome assembly

Cellular Component:
GO:0005737 cytoplasm
GO:0005789 endoplasmic reticulum membrane
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0032991 macromolecular complex


-  Descriptions from all associated GenBank mRNAs
  AK021928 - Homo sapiens cDNA FLJ11866 fis, clone HEMBA1006973, highly similar to Homo sapiens rab3-GAP regulatory domain mRNA.
AF255648 - Homo sapiens rGAP-iso mRNA, complete cds.
BC036513 - Homo sapiens cDNA clone IMAGE:4822549, containing frame-shift errors.
AL117631 - Homo sapiens mRNA; cDNA DKFZp434D245 (from clone DKFZp434D245); partial cds.
BC146760 - Homo sapiens RAB3 GTPase activating protein subunit 2 (non-catalytic), mRNA (cDNA clone MGC:166829 IMAGE:9007199), complete cds.
AK027485 - Homo sapiens cDNA FLJ14579 fis, clone NT2RM4001203, highly similar to Rab3 GTPase-activating protein non-catalytic subunit.
AB020646 - Homo sapiens KIAA0839 mRNA for KIAA0839 protein.
BC098383 - Homo sapiens cDNA clone IMAGE:30520261, containing frame-shift errors.
BC131573 - Homo sapiens cDNA clone IMAGE:40108635.
AK291234 - Homo sapiens cDNA FLJ78421 complete cds, highly similar to Homo sapiens RAB3 GTPase activating protein subunit 2 (non-catalytic) (RAB3GAP2), mRNA.
AF004828 - Homo sapiens rab3-GAP regulatory domain mRNA, complete cds.
AB384006 - Synthetic construct DNA, clone: pF1KSDA0839, Homo sapiens RAB3GAP2 gene for RAB3 GTPase-activating protein non-catalytic subunit, complete cds, without stop codon, in Flexi system.
AK074489 - Homo sapiens cDNA FLJ90008 fis, clone HEMBA1000275.
JD034228 - Sequence 15252 from Patent EP1572962.
JD546838 - Sequence 527862 from Patent EP1572962.
JD280267 - Sequence 261291 from Patent EP1572962.
JD089808 - Sequence 70832 from Patent EP1572962.
JD562695 - Sequence 543719 from Patent EP1572962.
JD049223 - Sequence 30247 from Patent EP1572962.
JD310079 - Sequence 291103 from Patent EP1572962.
BC050630 - Homo sapiens cDNA clone IMAGE:5580410, containing frame-shift errors.
JD108759 - Sequence 89783 from Patent EP1572962.
JD376199 - Sequence 357223 from Patent EP1572962.
JD404897 - Sequence 385921 from Patent EP1572962.
JD462534 - Sequence 443558 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9H2M9 (Reactome details) participates in the following event(s):

R-HSA-8850040 RAB3GAP1:RAB3GAP2 recruits RAB18:GCDP to ER
R-HSA-8850041 RAB3GAP1:RAB3GAP2 promotes nucleotide exchange on RAB18
R-HSA-8877998 RAB3GAP1:RAB3GAP2 exchanges GTP for GDP on RAB18
R-HSA-6811436 COPI-independent Golgi-to-ER retrograde traffic
R-HSA-8856688 Golgi-to-ER retrograde transport
R-HSA-8876198 RAB GEFs exchange GTP for GDP on RABs
R-HSA-6811442 Intra-Golgi and retrograde Golgi-to-ER traffic
R-HSA-9007101 Rab regulation of trafficking
R-HSA-199991 Membrane Trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: A6H8V0, KIAA0839, NM_012414, NP_036546, O75872, Q9H2M9, Q9HAB0, Q9UFJ7, Q9UQ15, RBGPR_HUMAN
UCSC ID: uc010puk.1
RefSeq Accession: NM_012414
Protein: Q9H2M9 (aka RBGPR_HUMAN)
CCDS: CCDS31028.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene RAB3GAP2:
rab18-def (RAB18 Deficiency)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_012414.3
exon count: 35CDS single in 3' UTR: no RNA size: 7329
ORF size: 4182CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 8564.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.