Human Gene RAB3GAP2 (uc010pum.1)
  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].
Transcript (Including UTRs)
   Position: hg19 chr1:220,382,749-220,445,843 Size: 63,095 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr1:220,383,721-220,445,679 Size: 61,959 Coding Exon Count: 7 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:220,382,749-220,445,843)mRNA (may differ from genome)Protein (206 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGeneCardsGeneNetworkH-INV
HGNCLynxMalacardsMGIPubMedReactome
UniProtKBWikipedia

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  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 -226.47972-0.233 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
  Pfam Domains:
PF14655 - Rab3 GTPase-activating protein regulatory subunit N-terminus

ModBase Predicted Comparative 3D Structure on Q9H2M9-2
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     
      
      
      

-  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.
BC146760 - Homo sapiens RAB3 GTPase activating protein subunit 2 (non-catalytic), mRNA (cDNA clone MGC:166829 IMAGE:9007199), complete cds.
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.
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: AK021928, KIAA0839, Q9H2M9-2
UCSC ID: uc010pum.1
RefSeq Accession: NM_012414
Protein: Q9H2M9-2, splice isoform of Q9H2M9

-  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: AK021928.1
exon count: 7CDS single in 3' UTR: no RNA size: 1852
ORF size: 621CDS single in intron: no Alignment % ID: 99.89
txCdsPredict score: 1442.00frame shift in genome: no % Coverage: 91.04
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: 981# 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.