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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 VWA3B

check button Gene summary
Gene informationGene symbol

VWA3B

Gene ID

200403

Gene namevon Willebrand factor A domain containing 3B
SynonymsSCAR22
Cytomap

2q11.2

Type of geneprotein-coding
Descriptionvon Willebrand factor A domain-containing protein 3BVWA domain-containing protein 3B
Modification date20180519
UniProtAcc

Q502W6

ContextPubMed: VWA3B [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 VWA3B 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 VWA3B

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 VWA3B

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_327921298709523:98709751:98715685:98715802:98732114:9873220998715685:98715802ENSG00000168658.14ENST00000484571.1
exon_skip_327922298732114:98732209:98735975:98736226:98737761:9873787598735975:98736226ENSG00000168658.14ENST00000416277.1,ENST00000448638.1,ENST00000433678.1,ENST00000409460.1,ENST00000477737.1,ENST00000435344.1
exon_skip_327923298732114:98732209:98735982:98736226:98737761:9873787598735982:98736226ENSG00000168658.14ENST00000432242.1
exon_skip_327925298737761:98737921:98744701:98744871:98750286:9875036098744701:98744871ENSG00000168658.14ENST00000416277.1,ENST00000433678.1,ENST00000409460.1,ENST00000477737.1,ENST00000432242.1,ENST00000435344.1,ENST00000422503.2,ENST00000451075.2
exon_skip_327928298744701:98744871:98750286:98750402:98779313:9877943998750286:98750402ENSG00000168658.14ENST00000416277.1,ENST00000433678.1,ENST00000409460.1,ENST00000477737.1,ENST00000432242.1,ENST00000435344.1,ENST00000422503.2,ENST00000451075.2
exon_skip_327929298750286:98750402:98779313:98779439:98797478:9879767598779313:98779439ENSG00000168658.14ENST00000433678.1,ENST00000409460.1,ENST00000477737.1,ENST00000432242.1,ENST00000435344.1,ENST00000422503.2,ENST00000451075.2
exon_skip_327930298779313:98779439:98795706:98795780:98797478:9879767598795706:98795780ENSG00000168658.14ENST00000416277.1
exon_skip_327931298797478:98797675:98804437:98804592:98809360:9880949998804437:98804592ENSG00000168658.14ENST00000433678.1,ENST00000409460.1,ENST00000477737.1,ENST00000435344.1,ENST00000422503.2,ENST00000451075.2
exon_skip_327932298828392:98828491:98833217:98833438:98834308:9883449198833217:98833438ENSG00000168658.14ENST00000433678.1,ENST00000432242.1,ENST00000495571.1
exon_skip_327933298834308:98834491:98844664:98844795:98846512:9884667098844664:98844795ENSG00000168658.14ENST00000416277.1,ENST00000448638.1,ENST00000409460.1,ENST00000473149.1,ENST00000477737.1,ENST00000432242.1,ENST00000495571.1
exon_skip_327934298851110:98851230:98852852:98852940:98853036:9885326798852852:98852940ENSG00000168658.14ENST00000416277.1,ENST00000448638.1,ENST00000409460.1,ENST00000473149.1,ENST00000477737.1,ENST00000432242.1,ENST00000495571.1,ENST00000489630.1
exon_skip_327936298866780:98866899:98872586:98872637:98887144:9888734698872586:98872637ENSG00000168658.14ENST00000490947.2,ENST00000409460.1,ENST00000473149.1,ENST00000477737.1,ENST00000495571.1,ENST00000489630.1
exon_skip_327938298914369:98914494:98916541:98916679:98920164:9892026598916541:98916679ENSG00000168658.14ENST00000490947.2,ENST00000473149.1,ENST00000477737.1,ENST00000432242.1,ENST00000495571.1,ENST00000489630.1
exon_skip_327939298916541:98916679:98920164:98920265:98928281:9892846498920164:98920265ENSG00000168658.14ENST00000490947.2,ENST00000473149.1,ENST00000477737.1,ENST00000432242.1,ENST00000495571.1,ENST00000489630.1
exon_skip_327941298920164:98920265:98928281:98928495:98928662:9892890498928281:98928495ENSG00000168658.14ENST00000477737.1,ENST00000432242.1,ENST00000495571.1,ENST00000489630.1

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

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Exon skipping events with PSIs in GTEx for VWA3B

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_327921298709523:98709751:98715685:98715802:98732114:9873220998715685:98715802ENSG00000168658.14ENST00000484571.1
exon_skip_327922298732114:98732209:98735975:98736226:98737761:9873787598735975:98736226ENSG00000168658.14ENST00000435344.1,ENST00000433678.1,ENST00000448638.1,ENST00000409460.1,ENST00000477737.1,ENST00000416277.1
exon_skip_327923298732114:98732209:98735982:98736226:98737761:9873787598735982:98736226ENSG00000168658.14ENST00000432242.1
exon_skip_327925298737761:98737921:98744701:98744871:98750286:9875036098744701:98744871ENSG00000168658.14ENST00000432242.1,ENST00000435344.1,ENST00000433678.1,ENST00000409460.1,ENST00000477737.1,ENST00000422503.2,ENST00000416277.1,ENST00000451075.2
exon_skip_327928298744701:98744871:98750286:98750402:98779313:9877943998750286:98750402ENSG00000168658.14ENST00000432242.1,ENST00000435344.1,ENST00000433678.1,ENST00000409460.1,ENST00000477737.1,ENST00000422503.2,ENST00000416277.1,ENST00000451075.2
exon_skip_327929298750286:98750402:98779313:98779439:98797478:9879767598779313:98779439ENSG00000168658.14ENST00000432242.1,ENST00000435344.1,ENST00000433678.1,ENST00000409460.1,ENST00000477737.1,ENST00000422503.2,ENST00000451075.2
exon_skip_327930298779313:98779439:98795706:98795780:98797478:9879767598795706:98795780ENSG00000168658.14ENST00000416277.1
exon_skip_327931298797478:98797675:98804437:98804592:98809360:9880949998804437:98804592ENSG00000168658.14ENST00000435344.1,ENST00000433678.1,ENST00000409460.1,ENST00000477737.1,ENST00000422503.2,ENST00000451075.2
exon_skip_327932298828392:98828491:98833217:98833438:98834308:9883449198833217:98833438ENSG00000168658.14ENST00000432242.1,ENST00000433678.1,ENST00000495571.1
exon_skip_327933298834308:98834491:98844664:98844795:98846512:9884667098844664:98844795ENSG00000168658.14ENST00000432242.1,ENST00000448638.1,ENST00000409460.1,ENST00000477737.1,ENST00000416277.1,ENST00000495571.1,ENST00000473149.1
exon_skip_327934298851110:98851230:98852852:98852940:98853036:9885326798852852:98852940ENSG00000168658.14ENST00000432242.1,ENST00000448638.1,ENST00000409460.1,ENST00000477737.1,ENST00000416277.1,ENST00000495571.1,ENST00000489630.1,ENST00000473149.1
exon_skip_327936298866780:98866899:98872586:98872637:98887144:9888734698872586:98872637ENSG00000168658.14ENST00000409460.1,ENST00000477737.1,ENST00000495571.1,ENST00000489630.1,ENST00000473149.1,ENST00000490947.2
exon_skip_327937298872586:98872637:98885804:98885954:98887144:9888734698885804:98885954ENSG00000168658.14ENST00000432242.1
exon_skip_327938298914369:98914494:98916541:98916679:98920164:9892026598916541:98916679ENSG00000168658.14ENST00000432242.1,ENST00000477737.1,ENST00000495571.1,ENST00000489630.1,ENST00000473149.1,ENST00000490947.2
exon_skip_327939298916541:98916679:98920164:98920265:98928281:9892846498920164:98920265ENSG00000168658.14ENST00000432242.1,ENST00000477737.1,ENST00000495571.1,ENST00000489630.1,ENST00000473149.1,ENST00000490947.2
exon_skip_327941298920164:98920265:98928281:98928495:98928662:9892890498928281:98928495ENSG00000168658.14ENST00000432242.1,ENST00000477737.1,ENST00000495571.1,ENST00000489630.1

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 VWA3B

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
ENST000004777379873597598736226Frame-shift
ENST000004777379874470198744871Frame-shift
ENST000004777379875028698750402Frame-shift
ENST000004777379880443798804592Frame-shift
ENST000004777379884466498844795Frame-shift
ENST000004777379885285298852940Frame-shift
ENST000004777379892016498920265Frame-shift
ENST000004777379892828198928495Frame-shift
ENST000004777379877931398779439In-frame
ENST000004777379887258698872637In-frame
ENST000004777379891654198916679In-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
ENST000004777379873597598736226Frame-shift
ENST000004777379874470198744871Frame-shift
ENST000004777379875028698750402Frame-shift
ENST000004777379880443798804592Frame-shift
ENST000004777379884466498844795Frame-shift
ENST000004777379885285298852940Frame-shift
ENST000004777379892016498920265Frame-shift
ENST000004777379892828198928495Frame-shift
ENST000004777379877931398779439In-frame
ENST000004777379887258698872637In-frame
ENST000004777379891654198916679In-frame

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Infer the effects of exon skipping event on protein functional features for VWA3B

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
ENST0000047773744711294987793139877943911931318329371
ENST0000047773744711294988725869887263729973047931947
ENST000004777374471129498916541989166793487362410941140

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
ENST0000047773744711294987793139877943911931318329371
ENST0000047773744711294988725869887263729973047931947
ENST000004777374471129498916541989166793487362410941140

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


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


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SNVs in the skipped exons for VWA3B

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_327923
exon_skip_327922
98735976987362269873601798736017Frame_Shift_DelT-p.H111fs
LIHCTCGA-DD-A1EG-01exon_skip_327923
exon_skip_327922
98735983987362269873601798736017Frame_Shift_DelT-p.H111fs
LUADTCGA-95-A4VN-01exon_skip_327925
98744702987448719874472898744728Frame_Shift_DelG-p.V243fs
LIHCTCGA-G3-A3CJ-01exon_skip_327925
98744702987448719874484298744842Frame_Shift_DelA-p.L281fs
LIHCTCGA-DD-A3A0-01exon_skip_327938
98916542989166799891656398916563Frame_Shift_DelA-p.K1102fs
LIHCTCGA-DD-A3A0-01exon_skip_327939
98920165989202659892024098920240Frame_Shift_DelC-p.P1167fs
LIHCTCGA-DD-A1EG-01exon_skip_327941
98928282989284959892847498928474Frame_Shift_DelG-p.Q1238fs
LUSCTCGA-22-5473-01exon_skip_327925
98744702987448719874474198744741Nonsense_MutationGTp.E248*
PAADTCGA-IB-7651-01exon_skip_327928
98750287987504029875032198750321Nonsense_MutationGTp.E303*
PAADTCGA-IB-7651-01exon_skip_327928
98750287987504029875032198750321Nonsense_MutationGTp.E303X
SKCMTCGA-EB-A51B-01exon_skip_327933
98844665988447959884476298844762Nonsense_MutationGAp.W706*
SKCMTCGA-EB-A3XF-01exon_skip_327941
98928282989284959892832898928328Nonsense_MutationATp.K1190*
UCECTCGA-BS-A0UJ-01exon_skip_327941
98928282989284959892836198928361Nonsense_MutationATp.R1201*
LIHCTCGA-2Y-A9GT-01exon_skip_327929
98779314987794399877944098779440Splice_SiteGA.
SARCTCGA-QC-A7B5-01exon_skip_327931
98804438988045929880443798804437Splice_SiteGAe9-1
LUSCTCGA-18-3409-01exon_skip_327934
98852853988529409885294298852942Splice_SiteTGp.D839_splice

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
FEPD_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE98920165989202659892023098920230Frame_Shift_DelT-p.H1162fs
NCIH196_LUNG98735983987362269873606698736067Frame_Shift_Ins-Gp.S128fs
NCIH196_LUNG98735976987362269873606698736067Frame_Shift_Ins-Gp.S128fs
HCC2450_LUNG98735983987362269873616398736163Missense_MutationGAp.R160Q
HCC2450_LUNG98735976987362269873616398736163Missense_MutationGAp.R160Q
HCC366_LUNG98735983987362269873620598736205Missense_MutationTAp.I174K
HCC366_LUNG98735976987362269873620598736205Missense_MutationTAp.I174K
NCIH1770_LUNG98744702987448719874471498744714Missense_MutationTAp.Y239N
SBC1_LUNG98750287987504029875035898750358Missense_MutationTCp.V315A
GRST_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE98779314987794399877933498779334Missense_MutationGAp.V337M
SNU81_LARGE_INTESTINE98779314987794399877933798779337Missense_MutationTCp.F338L
CW2_LARGE_INTESTINE98804438988045929880445798804457Missense_MutationTAp.V444D
KE37_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE98804438988045929880458098804580Missense_MutationGAp.R485Q
MERO84_LUNG98804438988045929880458698804586Missense_MutationGAp.R487Q
MCCAR_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE98804438988045929880458698804586Missense_MutationGAp.R487Q
IGR1_SKIN98844665988447959884469298844692Missense_MutationGAp.E683K
LNCAPCLONEFGC_PROSTATE98844665988447959884472798844727Missense_MutationGAp.M694I
NCIH2085_LUNG98844665988447959884473198844731Missense_MutationGTp.D696Y
MIAPACA2_PANCREAS98852853988529409885289598852895Missense_MutationCTp.S824L
PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE98872587988726379887259698872596Missense_MutationTGp.N934K
BE13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE98872587988726379887259698872596Missense_MutationTGp.N934K
LOVO_LARGE_INTESTINE98872587988726379887259798872597Missense_MutationAGp.K935E
PEER_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE98872587988726379887261398872613Missense_MutationCAp.A940E
BE13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE98872587988726379887261398872613Missense_MutationCAp.A940E
NCIH211_LUNG98916542989166799891654698916546Missense_MutationGAp.G1096E
ES8_BONE98916542989166799891661598916615Missense_MutationCAp.A1119E
SNU719_STOMACH98920165989202659892019398920193Missense_MutationACp.K1150T
NCIH2347_LUNG98920165989202659892024498920244Missense_MutationCAp.P1167Q
HCC2450_LUNG98920165989202659892026198920261Missense_MutationGCp.E1173Q
SKGT2_STOMACH98928282989284959892833598928335Missense_MutationCTp.A1192V
HT115_LARGE_INTESTINE98928282989284959892836598928365Missense_MutationGAp.R1202Q
ES2_OVARY98928282989284959892838098928380Missense_MutationGTp.R1207M
PACADD137_PANCREAS98928282989284959892843698928436Missense_MutationGAp.G1226S
EKVX_LUNG98928282989284959892846398928463Missense_MutationGCp.G1235R
D542MG_CENTRAL_NERVOUS_SYSTEM98804438988045929880454798804547Nonsense_MutationGAp.W474*
MIAPACA2_PANCREAS98852853988529409885289898852898Nonsense_MutationCGp.S825*
NCIH1563_LUNG98872587988726379887262198872621Nonsense_MutationCTp.Q943*
JHH6_LIVER98744702987448719874470298744702Splice_SiteAGp.I235V
KYSE140_OESOPHAGUS98744702987448719874470298744702Splice_SiteAGp.I235V
NUGC2_STOMACH98744702987448719874470298744702Splice_SiteAGp.I235V
SNU61_LARGE_INTESTINE98744702987448719874470298744702Splice_SiteAGp.I235V
KYSE450_OESOPHAGUS98744702987448719874470298744702Splice_SiteAGp.I235V
RCC10RGB_KIDNEY98744702987448719874470298744702Splice_SiteAGp.I235V
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE98779314987794399877943898779438Splice_SiteCTp.C371C

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for VWA3B

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 VWA3B


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for VWA3B


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RelatedDrugs for VWA3B

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 VWA3B

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource