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Center for Computational Systems Medicine
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Gene summary

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Gene structures and expression levels

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Exon skipping events with PSIs in TCGA

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Exon skipping events with PSIs in GTEx

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Open reading frame (ORF) annotation in the exon skipping event

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Exon skipping events in the canonical protein sequence

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SNVs in the skipped exons with depth of coverage

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon

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Related drugs with this gene

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Related diseases with this gene

Gene summary for RAB3GAP2

check button Gene summary
Gene informationGene symbol

RAB3GAP2

Gene ID

25782

Gene nameRAB3 GTPase activating non-catalytic protein subunit 2
SynonymsRAB3-GAP150|RAB3GAP150|SPG69|WARBM2|p150
Cytomap

1q41

Type of geneprotein-coding
Descriptionrab3 GTPase-activating protein non-catalytic subunitRAB3 GTPase activating protein subunit 2 (non-catalytic)RGAP-isorab3 GTPase-activating protein 150 kDa subunitrab3-GAP p150rab3-GAP regulatory subunit
Modification date20180523
UniProtAcc

Q9H2M9

ContextPubMed: RAB3GAP2 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract]
- Title (PMID)

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID

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Exon skipping events across known transcript of Ensembl for RAB3GAP2 from UCSC genome browser

check buttonSkipped exons in TCGA and GTEx based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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Gene isoform structures and expression levels for RAB3GAP2

check button Expression levels of gene isoforms across TCGA.
gencode gene structure

check button Expression levels of gene isoforms across GTEx.
gencode gene structure


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Exon skipping events with PSIs in TCGA for RAB3GAP2

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_370931220324597:220324748:220324947:220325106:220326526:220326748220324947:220325106ENSG00000118873.11ENST00000474966.1,ENST00000358951.2
exon_skip_370941220324947:220325106:220326526:220326748:220327309:220327399220326526:220326748ENSG00000118873.11ENST00000491305.1,ENST00000491005.1,ENST00000358951.2
exon_skip_370971220330611:220330830:220331143:220331218:220332727:220332763220331143:220331218ENSG00000118873.11ENST00000358951.2
exon_skip_370981220331143:220331218:220332727:220332763:220335539:220335610220332727:220332763ENSG00000118873.11ENST00000358951.2
exon_skip_370991220332727:220332763:220335539:220335610:220338074:220338137220335539:220335610ENSG00000118873.11ENST00000358951.2
exon_skip_371051220335539:220335610:220338074:220338141:220340634:220340741220338074:220338141ENSG00000118873.11ENST00000358951.2
exon_skip_371061220357377:220357505:220358992:220359083:220363044:220363109220358992:220359083ENSG00000118873.11ENST00000358951.2
exon_skip_371071220368639:220368719:220369591:220369740:220375617:220375716220369591:220369740ENSG00000118873.11ENST00000358951.2
exon_skip_371091220369591:220369740:220375617:220375716:220379248:220379348220375617:220375716ENSG00000118873.11ENST00000358951.2,ENST00000237724.5
exon_skip_371111220379248:220379348:220383729:220383831:220384142:220384218220383729:220383831ENSG00000118873.11ENST00000484658.1,ENST00000474178.1,ENST00000358951.2
exon_skip_371131220383729:220383831:220384142:220384218:220384296:220384344220384142:220384218ENSG00000118873.11ENST00000484658.1,ENST00000474178.1,ENST00000358951.2
exon_skip_371151220384142:220384218:220384296:220384344:220386228:220386310220384296:220384344ENSG00000118873.11ENST00000358951.2

check button PSI values of skipped exons in TCGA.
psi tcga

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Exon skipping events with PSIs in GTEx for RAB3GAP2

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_370931220324597:220324748:220324947:220325106:220326526:220326748220324947:220325106ENSG00000118873.11ENST00000358951.2,ENST00000474966.1
exon_skip_370941220324947:220325106:220326526:220326748:220327309:220327399220326526:220326748ENSG00000118873.11ENST00000358951.2,ENST00000491005.1,ENST00000491305.1
exon_skip_370971220330611:220330830:220331143:220331218:220332727:220332763220331143:220331218ENSG00000118873.11ENST00000358951.2
exon_skip_370981220331143:220331218:220332727:220332763:220335539:220335610220332727:220332763ENSG00000118873.11ENST00000358951.2
exon_skip_370991220332727:220332763:220335539:220335610:220338074:220338137220335539:220335610ENSG00000118873.11ENST00000358951.2
exon_skip_371051220335539:220335610:220338074:220338141:220340634:220340741220338074:220338141ENSG00000118873.11ENST00000358951.2
exon_skip_371061220357377:220357505:220358992:220359083:220363044:220363109220358992:220359083ENSG00000118873.11ENST00000358951.2
exon_skip_371071220368639:220368719:220369591:220369740:220375617:220375716220369591:220369740ENSG00000118873.11ENST00000358951.2
exon_skip_371091220369591:220369740:220375617:220375716:220379248:220379348220375617:220375716ENSG00000118873.11ENST00000358951.2,ENST00000237724.5
exon_skip_371111220379248:220379348:220383729:220383831:220384142:220384218220383729:220383831ENSG00000118873.11ENST00000358951.2,ENST00000484658.1,ENST00000474178.1
exon_skip_371131220383729:220383831:220384142:220384218:220384296:220384344220384142:220384218ENSG00000118873.11ENST00000358951.2,ENST00000484658.1,ENST00000474178.1
exon_skip_371151220384142:220384218:220384296:220384344:220386228:220386310220384296:220384344ENSG00000118873.11ENST00000358951.2

check button PSI values of skipped exons in GTEx.
psi gtex

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for RAB3GAP2

check button Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST00000358951220335539220335610Frame-shift
ENST00000358951220338074220338141Frame-shift
ENST00000358951220358992220359083Frame-shift
ENST00000358951220369591220369740Frame-shift
ENST00000358951220384142220384218Frame-shift
ENST00000358951220324947220325106In-frame
ENST00000358951220326526220326748In-frame
ENST00000358951220331143220331218In-frame
ENST00000358951220332727220332763In-frame
ENST00000358951220375617220375716In-frame
ENST00000358951220383729220383831In-frame
ENST00000358951220384296220384344In-frame

check button Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST00000358951220335539220335610Frame-shift
ENST00000358951220338074220338141Frame-shift
ENST00000358951220358992220359083Frame-shift
ENST00000358951220369591220369740Frame-shift
ENST00000358951220384142220384218Frame-shift
ENST00000358951220324947220325106In-frame
ENST00000358951220326526220326748In-frame
ENST00000358951220331143220331218In-frame
ENST00000358951220332727220332763In-frame
ENST00000358951220375617220375716In-frame
ENST00000358951220383729220383831In-frame
ENST00000358951220384296220384344In-frame

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Infer the effects of exon skipping event on protein functional features for RAB3GAP2

check button Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.
prot feature distribution

check button Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST0000035895172741393220384296220384344504551129144
ENST0000035895172741393220383729220383831628729170204
ENST0000035895172741393220375617220375716830928237270
ENST00000358951727413932203327272203327633343337810751087
ENST00000358951727413932203311432203312183379345310871112
ENST00000358951727413932203265262203267483763398412151289
ENST00000358951727413932203249472203251063985414312891342

check button Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST0000035895172741393220384296220384344504551129144
ENST0000035895172741393220383729220383831628729170204
ENST0000035895172741393220375617220375716830928237270
ENST00000358951727413932203327272203327633343337810751087
ENST00000358951727413932203311432203312183379345310871112
ENST00000358951727413932203265262203267483763398412151289
ENST00000358951727413932203249472203251063985414312891342

check button Lost protein functional features of individual exon skipping events in TCGA.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
Q9H2M912914411393ChainID=PRO_0000191662;Note=Rab3 GTPase-activating protein non-catalytic subunit
Q9H2M917020411393ChainID=PRO_0000191662;Note=Rab3 GTPase-activating protein non-catalytic subunit
Q9H2M92372702071393Alternative sequenceID=VSP_013312;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q9H2M923727011393ChainID=PRO_0000191662;Note=Rab3 GTPase-activating protein non-catalytic subunit
Q9H2M9107510872071393Alternative sequenceID=VSP_013312;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q9H2M91075108711393ChainID=PRO_0000191662;Note=Rab3 GTPase-activating protein non-catalytic subunit
Q9H2M9108711122071393Alternative sequenceID=VSP_013312;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q9H2M91087111211393ChainID=PRO_0000191662;Note=Rab3 GTPase-activating protein non-catalytic subunit
Q9H2M91087111210921092Natural variantID=VAR_021589;Note=S->T;Dbxref=dbSNP:rs2289189
Q9H2M9121512892071393Alternative sequenceID=VSP_013312;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q9H2M91215128911393ChainID=PRO_0000191662;Note=Rab3 GTPase-activating protein non-catalytic subunit
Q9H2M9128913422071393Alternative sequenceID=VSP_013312;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q9H2M91289134211393ChainID=PRO_0000191662;Note=Rab3 GTPase-activating protein non-catalytic subunit


check button Lost protein functional features of individual exon skipping events in GTEx.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
Q9H2M912914411393ChainID=PRO_0000191662;Note=Rab3 GTPase-activating protein non-catalytic subunit
Q9H2M917020411393ChainID=PRO_0000191662;Note=Rab3 GTPase-activating protein non-catalytic subunit
Q9H2M92372702071393Alternative sequenceID=VSP_013312;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q9H2M923727011393ChainID=PRO_0000191662;Note=Rab3 GTPase-activating protein non-catalytic subunit
Q9H2M9107510872071393Alternative sequenceID=VSP_013312;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q9H2M91075108711393ChainID=PRO_0000191662;Note=Rab3 GTPase-activating protein non-catalytic subunit
Q9H2M9108711122071393Alternative sequenceID=VSP_013312;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q9H2M91087111211393ChainID=PRO_0000191662;Note=Rab3 GTPase-activating protein non-catalytic subunit
Q9H2M91087111210921092Natural variantID=VAR_021589;Note=S->T;Dbxref=dbSNP:rs2289189
Q9H2M9121512892071393Alternative sequenceID=VSP_013312;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q9H2M91215128911393ChainID=PRO_0000191662;Note=Rab3 GTPase-activating protein non-catalytic subunit
Q9H2M9128913422071393Alternative sequenceID=VSP_013312;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
Q9H2M91289134211393ChainID=PRO_0000191662;Note=Rab3 GTPase-activating protein non-catalytic subunit


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SNVs in the skipped exons for RAB3GAP2

check button - Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.
lollipop

check button - Differential PSIs between mutated versus non-mutated samples.

check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
LIHCTCGA-DD-A1EG-01exon_skip_37093
220324948220325106220325047220325047Frame_Shift_DelC-p.G1309fs
LIHCTCGA-DD-A3A0-01exon_skip_37094
220326527220326748220326565220326565Frame_Shift_DelC-p.E1277fs
LIHCTCGA-DD-A39Y-01exon_skip_37105
220338075220338141220338099220338099Frame_Shift_DelT-p.I1044fs
LIHCTCGA-G3-A3CJ-01exon_skip_37105
220338075220338141220338127220338127Frame_Shift_DelA-p.F1034fs
STADTCGA-HF-A5NB-01exon_skip_37105
220338075220338141220338127220338127Frame_Shift_DelA-p.F1034fs
STADTCGA-HF-A5NB-01exon_skip_37105
220338075220338141220338127220338127Frame_Shift_DelA-p.V1035fs
STADTCGA-HU-A4GQ-01exon_skip_37105
220338075220338141220338127220338127Frame_Shift_DelA-p.F1034fs
STADTCGA-HU-A4GQ-01exon_skip_37105
220338075220338141220338127220338127Frame_Shift_DelA-p.V1035fs
LIHCTCGA-DD-A39Y-01exon_skip_37107
220369592220369740220369697220369697Frame_Shift_DelG-p.S285fs
LIHCTCGA-DD-A3A0-01exon_skip_37113
220384143220384218220384173220384173Frame_Shift_DelA-p.F160fs
LIHCTCGA-G3-A3CJ-01exon_skip_37113
220384143220384218220384173220384173Frame_Shift_DelA-p.F160fs
COADTCGA-AA-3663-01exon_skip_37105
220338075220338141220338126220338127Frame_Shift_Ins-Ap.V1035fs
STADTCGA-BR-8487-01exon_skip_37107
220369592220369740220369665220369666Frame_Shift_Ins-Tp.N296fs
BLCATCGA-KQ-A41P-01exon_skip_37093
220324948220325106220325067220325067Nonsense_MutationGAp.Q1303*
UCECTCGA-B5-A0JY-01exon_skip_37109
220375618220375716220375667220375667Nonsense_MutationCAp.E156*
COADTCGA-AZ-6601-01exon_skip_37111
220383730220383831220383753220383753Nonsense_MutationGAp.R197X
KIRCTCGA-B8-4143-01exon_skip_37094
220326527220326748220326526220326526Splice_SiteCT.
SKCMTCGA-EE-A2GC-06exon_skip_37111
220383730220383831220383832220383832Splice_SiteCT.

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
ISHIKAWAHERAKLIO02ER_ENDOMETRIUM220338075220338141220338127220338127Frame_Shift_DelA-p.F1034fs
SNUC5_LARGE_INTESTINE220338075220338141220338127220338127Frame_Shift_DelA-p.F1034fs
DOK_UPPER_AERODIGESTIVE_TRACT220324948220325106220325034220325034Missense_MutationGAp.H1314Y
JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE220326527220326748220326633220326633Missense_MutationGAp.A1254V
HEC108_ENDOMETRIUM220326527220326748220326664220326664Missense_MutationTCp.T1244A
KGN_OVARY220326527220326748220326670220326670Missense_MutationTCp.T1242A
TGBC11TKB_STOMACH220326527220326748220326699220326699Missense_MutationGAp.T1232I
CH157MN_CENTRAL_NERVOUS_SYSTEM220326527220326748220326700220326700Missense_MutationTCp.T1232A
SNU1040_LARGE_INTESTINE220332728220332763220332735220332735Missense_MutationCTp.C1085Y
EN_ENDOMETRIUM220332728220332763220332742220332742Missense_MutationTCp.R1083G
EN_ENDOMETRIUM220358993220359083220359028220359028Missense_MutationAGp.I612T
SW1783_CENTRAL_NERVOUS_SYSTEM220358993220359083220359055220359055Missense_MutationCTp.R603H
ISTMES2_PLEURA220358993220359083220359056220359056Missense_MutationGAp.R603C
RERFLCAD2_LUNG220369592220369740220369659220369659Missense_MutationGAp.P298L
RH1_SOFT_TISSUE220375618220375716220375660220375660Missense_MutationCAp.G257C
HT115_LARGE_INTESTINE220383730220383831220383752220383752Missense_MutationCTp.R197Q
CORL47_LUNG220384143220384218220384204220384204Missense_MutationCAp.R150L

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RAB3GAP2

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RAB3GAP2


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RAB3GAP2


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RelatedDrugs for RAB3GAP2

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
GeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for RAB3GAP2

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
RAB3GAP2C0796037Martsolf syndrome1CTD_human;ORPHANET;UNIPROT