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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 5111

FusionGeneSummary for C9orf3_PTPDC1

check button Fusion gene summary
Fusion gene informationFusion gene name: C9orf3_PTPDC1
Fusion gene ID: 5111
HgeneTgene
Gene symbol

C9orf3

PTPDC1

Gene ID

84909

138639

Gene namechromosome 9 open reading frame 3protein tyrosine phosphatase domain containing 1
SynonymsAOPEP|AP-O|APO|C90RF3|ONPEPPTP9Q22
Cytomap

9q22.32

9q22.32

Type of geneprotein-codingprotein-coding
Descriptionaminopeptidase Oprotein tyrosine phosphatase domain-containing protein 1protein tyrosine phosphatase PTP9Q22
Modification date2018052320180523
UniProtAcc

A2A3K4

Ensembl transtripts involved in fusion geneENST00000277198, ENST00000297979, 
ENST00000375315, ENST00000395357, 
ENST00000425634, ENST00000433691, 
ENST00000473778, 		ENST00000375360, 
ENST00000288976, ENST00000467049, 
Fusion gene scores* DoF score12 X 11 X 7=9243 X 3 X 3=27
# samples 123
** MAII scorelog2(12/924*10)=-2.94485844580754
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: C9orf3 [Title/Abstract] AND PTPDC1 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneC9orf3

GO:0006508

proteolysis

15687497


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVBRCATCGA-C8-A12L-01AC9orf3chr9

97522862

+PTPDC1chr9

96827016

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
5CDS-5UTRENST00000277198ENST00000375360C9orf3chr9

97522862

+PTPDC1chr9

96827016

+
5CDS-intronENST00000277198ENST00000288976C9orf3chr9

97522862

+PTPDC1chr9

96827016

+
5CDS-intronENST00000277198ENST00000467049C9orf3chr9

97522862

+PTPDC1chr9

96827016

+
5CDS-5UTRENST00000297979ENST00000375360C9orf3chr9

97522862

+PTPDC1chr9

96827016

+
5CDS-intronENST00000297979ENST00000288976C9orf3chr9

97522862

+PTPDC1chr9

96827016

+
5CDS-intronENST00000297979ENST00000467049C9orf3chr9

97522862

+PTPDC1chr9

96827016

+
5CDS-5UTRENST00000375315ENST00000375360C9orf3chr9

97522862

+PTPDC1chr9

96827016

+
5CDS-intronENST00000375315ENST00000288976C9orf3chr9

97522862

+PTPDC1chr9

96827016

+
5CDS-intronENST00000375315ENST00000467049C9orf3chr9

97522862

+PTPDC1chr9

96827016

+
intron-5UTRENST00000395357ENST00000375360C9orf3chr9

97522862

+PTPDC1chr9

96827016

+
intron-intronENST00000395357ENST00000288976C9orf3chr9

97522862

+PTPDC1chr9

96827016

+
intron-intronENST00000395357ENST00000467049C9orf3chr9

97522862

+PTPDC1chr9

96827016

+
intron-5UTRENST00000425634ENST00000375360C9orf3chr9

97522862

+PTPDC1chr9

96827016

+
intron-intronENST00000425634ENST00000288976C9orf3chr9

97522862

+PTPDC1chr9

96827016

+
intron-intronENST00000425634ENST00000467049C9orf3chr9

97522862

+PTPDC1chr9

96827016

+
intron-5UTRENST00000433691ENST00000375360C9orf3chr9

97522862

+PTPDC1chr9

96827016

+
intron-intronENST00000433691ENST00000288976C9orf3chr9

97522862

+PTPDC1chr9

96827016

+
intron-intronENST00000433691ENST00000467049C9orf3chr9

97522862

+PTPDC1chr9

96827016

+
intron-5UTRENST00000473778ENST00000375360C9orf3chr9

97522862

+PTPDC1chr9

96827016

+
intron-intronENST00000473778ENST00000288976C9orf3chr9

97522862

+PTPDC1chr9

96827016

+
intron-intronENST00000473778ENST00000467049C9orf3chr9

97522862

+PTPDC1chr9

96827016

+

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FusionProtFeatures for C9orf3_PTPDC1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
C9orf3

PTPDC1

A2A3K4

Lectin that binds to various sugars: galactose > mannose= fucose > N-acetylglucosamine > N-acetylgalactosamine(PubMed:10224141). Acts as a chemoattractant, probably involved inthe regulation of cell migration (PubMed:28301481).{ECO:0000269|PubMed:10224141, ECO:0000269|PubMed:28301481}. May play roles in cilia formation and/or maintenance.{ECO:0000250}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page

.

* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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FusionGeneSequence for C9orf3_PTPDC1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for C9orf3_PTPDC1


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page

.

check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors
C9orf3SUN2, LRRC40, ZDHHC17, TUBA4A, SUZ12, TUBB3PTPDC1XPO1, FBXO3, HARS, MAPK1, MAPK3, PPP2CA, PPP2R1A, PPP2R2A, PPP2R2D, USP9X, YWHAQ, ARL2, CASK, PPP2R1B, PTPDC1, CSN3, MAPK1IP1L, DHPS, MAPKAPK3, YWHAH, PRPS1L1, TIPRL, PTGES3L, YWHAG, SDHB, YWHAB, CCNB1, YWHAZ, POLDIP2, CCDC28A, PCMT1, PPP2R2B, LMTK2, AATK, ERBB4, ERBB3, BBS12, DCAF7


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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RelatedDrugs for C9orf3_PTPDC1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for C9orf3_PTPDC1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneC9orf3C0004238Atrial Fibrillation1CTD_human
HgeneC9orf3C0032927Precancerous Conditions1CTD_human
HgeneC9orf3C3495559Juvenile arthritis1CTD_human