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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: 7312

FusionGeneSummary for CLCF1_PPP1CA

check button Fusion gene summary
Fusion gene informationFusion gene name: CLCF1_PPP1CA
Fusion gene ID: 7312
HgeneTgene
Gene symbol

CLCF1

PPP1CA

Gene ID

23529

5499

Gene namecardiotrophin like cytokine factor 1protein phosphatase 1 catalytic subunit alpha
SynonymsBSF-3|BSF3|CISS2|CLC|NNT-1|NNT1|NR6PP-1A|PP1A|PP1alpha|PPP1A
Cytomap

11q13.2

11q13.2

Type of geneprotein-codingprotein-coding
Descriptioncardiotrophin-like cytokine factor 1B-cell stimulatory factor 3B-cell-stimulating factor 3CRLF1 associated cytokine-like factor 1neurotrophin-1/B-cell stimulating factor-3novel neurotrophin-1serine/threonine-protein phosphatase PP1-alpha catalytic subunitprotein phosphatase 1, catalytic subunit, alpha isoformprotein phosphatase 1, catalytic subunit, alpha isozymeserine/threonine protein phosphatase PP1-alpha 1 catalytic subunittesticular
Modification date2018052320180522
UniProtAcc

Q9UBD9

P62136

Ensembl transtripts involved in fusion geneENST00000312438, ENST00000533438, 
ENST00000528474, 
ENST00000312989, 
ENST00000532446, ENST00000376745, 
ENST00000358239, 
Fusion gene scores* DoF score1 X 1 X 2=23 X 2 X 4=24
# samples 24
** MAII scorelog2(2/2*10)=3.32192809488736log2(4/24*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: CLCF1 [Title/Abstract] AND PPP1CA [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
HgeneCLCF1

GO:0008284

positive regulation of cell proliferation

10966616|11285233

HgeneCLCF1

GO:0042531

positive regulation of tyrosine phosphorylation of STAT protein

10966616|11285233

HgeneCLCF1

GO:0043524

negative regulation of neuron apoptotic process

10966616|11285233

TgenePPP1CA

GO:0016311

dephosphorylation

22311981


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
TCGARVKIRPTCGA-BQ-5890-01ACLCF1chr11

67140995

-PPP1CAchr11

67168670

-
TCGARVLUSCTCGA-NC-A5HK-01ACLCF1chr11

67140995

-PPP1CAchr11

67168670

-
* 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
Frame-shiftENST00000312438ENST00000312989CLCF1chr11

67140995

-PPP1CAchr11

67168670

-
5CDS-5UTRENST00000312438ENST00000532446CLCF1chr11

67140995

-PPP1CAchr11

67168670

-
5CDS-5UTRENST00000312438ENST00000376745CLCF1chr11

67140995

-PPP1CAchr11

67168670

-
5CDS-intronENST00000312438ENST00000358239CLCF1chr11

67140995

-PPP1CAchr11

67168670

-
intron-3CDSENST00000533438ENST00000312989CLCF1chr11

67140995

-PPP1CAchr11

67168670

-
intron-5UTRENST00000533438ENST00000532446CLCF1chr11

67140995

-PPP1CAchr11

67168670

-
intron-5UTRENST00000533438ENST00000376745CLCF1chr11

67140995

-PPP1CAchr11

67168670

-
intron-intronENST00000533438ENST00000358239CLCF1chr11

67140995

-PPP1CAchr11

67168670

-
intron-3CDSENST00000528474ENST00000312989CLCF1chr11

67140995

-PPP1CAchr11

67168670

-
intron-5UTRENST00000528474ENST00000532446CLCF1chr11

67140995

-PPP1CAchr11

67168670

-
intron-5UTRENST00000528474ENST00000376745CLCF1chr11

67140995

-PPP1CAchr11

67168670

-
intron-intronENST00000528474ENST00000358239CLCF1chr11

67140995

-PPP1CAchr11

67168670

-

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FusionProtFeatures for CLCF1_PPP1CA


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
CLCF1

Q9UBD9

PPP1CA

P62136

Cytokine with B-cell stimulating capability. Binds toand activates the ILST/gp130 receptor.{ECO:0000269|PubMed:10448081, ECO:0000269|PubMed:10500198}. Protein phosphatase that associates with over 200regulatory proteins to form highly specific holoenzymes whichdephosphorylate hundreds of biological targets. Proteinphosphatase 1 (PP1) is essential for cell division, andparticipates in the regulation of glycogen metabolism, musclecontractility and protein synthesis. Involved in regulation ofionic conductances and long-term synaptic plasticity. May play animportant role in dephosphorylating substrates such as thepostsynaptic density-associated Ca(2+)/calmodulin dependentprotein kinase II. Component of the PTW/PP1 phosphatase complex,which plays a role in the control of chromatin structure and cellcycle progression during the transition from mitosis intointerphase. Regulates NEK2 function in terms of kinase activityand centrosome number and splitting, both in the presence andabsence of radiation-induced DNA damage. Regulator of neural tubeand optic fissure closure, and enteric neural crest cell (ENCCs)migration during development. In balance with CSNK1D and CSNK1E,determines the circadian period length, through the regulation ofthe speed and rhythmicity of PER1 and PER2 phosphorylation. Maydephosphorylate CSNK1D and CSNK1E. Dephosphorylates the 'Ser-418'residue of FOXP3 in regulatory T-cells (Treg) from patients withrheumatoid arthritis, thereby inactivating FOXP3 and renderingTreg cells functionally defective (PubMed:23396208).Dephosphorylates CENPA (PubMed:25556658). Dephosphorylates the'Ser-139' residue of ATG16L1 causing dissociation of ATG12-ATG5-ATG16L1 complex, thereby inhibiting autophagy (PubMed:26083323).{ECO:0000269|PubMed:17283141, ECO:0000269|PubMed:21712997,ECO:0000269|PubMed:23396208, ECO:0000269|PubMed:25556658,ECO:0000269|PubMed:26083323}.

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 CLCF1_PPP1CA


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 CLCF1_PPP1CA


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
CLCF1CNTFR, CRLF1, PARK7PPP1CAPHACTR3, PHACTR1, ACTA1, EED, PPP1R8, PPP1R15A, AKAP11, GSK3B, SMARCB1, PPP1R9B, RYR2, EIF2AK2, KCNQ1, BCL2L1, BCL2L2, HSPA8, PPP1R10, NOC2L, RRP1B, HCFC1, LMTK2, CDC5L, BRCA1, RUVBL2, RPAP2, RPAP3, NCOR1, IKBKB, CUEDC2, CCDC6, CREB1, TRIM28, WDR82, TOX4, MYC, HDAC5, STAU1, NONO, SFPQ, AATK, CSRNP1, C1QA, CNST, TPRN, PPP1R18, TOR1AIP1, NEK2, PPP1R2, PPP1R3C, PPP1R3D, PPP1R3E, TP53BP2, PPP1R13B, PPP1R3G, PPP1R13L, PPP1R15B, PPP1R16A, RANBP9, RIF1, SH3RF2, WBP11, YLPM1, ZFYVE9, KANK1, BTBD10, CLCN2, CEP170, CLTC, CKB, CNP, CNTN1, CRK, CXXC1, DCTN1, DEAF1, FRMPD4, GLIPR1L2, GLTSCR2, IBTK, MIIP, JPH3, KCTD20, RPRD2, KIAA1377, LPIN2, MAFG, MAL2, MAP4K4, NDP, PHC1, PIAS1, PIAS3, PREX1, PRR16, SLC45A1, SNCAIP, SORL1, SPRED1, UBE2Z, ULK1, ZBTB11, ZNF827, SF3A2, SIRT7, TFG, ACTB, INA, PPP1R1B, ATM, AURKB, BCL2, PTK2, LBR, RB1, CDK1, CDK2, CDK4, CCNB1, CCND3, HSPA4, MAX, SKP1, STX1A, APAF1, CCNA1, PPP2R4, CDH1, PTEN, CUL1, BAD, WWTR1, CUL3, KIF13B, DCX, NCAM1, CAV1, AKT1, AURKA, PPP1CB, SRSF7, SRSF5, SRSF11, DDX1, SYNCRIP, VTN, OGT, SON, RPS24, TPBG, ZNF326, CHMP2A, SMARCA5, ESR1, ECT2, MDC1, MDM4, AXIN1, CSNK1E, PRKCB, TCTEX1D4, SFRP1, PPP1R32, FN1, VCAM1, CD2BP2, TOE1, GPKOW, GRB2, MPHOSPH10, PPP1R37, TP53, TUSC3, NOM1, PPP1R26, CCDC181, ZFYVE16, PPP1R3B, CASC5, KIF18A, STAM, CSRNP2, SYTL2, HEYL, PLCL2, ITGA4, PRKAR1A, MST1R, CTDP1, CHUK, TNFRSF1A, POLR2A, YAP1, MAT2B, PKM, ALDH7A1, ASNS, CAPNS1, STK24, TBCB, YWHAH, SCPEP1, TMOD3, XPO1, WWOX, HUWE1, PPP1R2P3, CUL7, OBSL1, CSNK2B, DEC1, RORC, CLOCK, PPP2R5E, ARNTL, PPP1R7, GPN3, PIH1D1, WDR92, PPP1CC, PDRG1, PPP1R9A, GYS2, GYS1, CDCA2, UXT, POLR3A, SCRIB, LRRC1, C12orf57, KIAA1279, MKI67, PEAK1, ERBB2IP, EIF2AK4, URI1, RUVBL1, SHOC2, NUP153, C20orf27, POLR2E, CCDC85C, RASSF8, GYG1, TANC2, PHACTR4, PPP1R11, CCDC85B, POLR3E, POLR3B, RASSF7, HOMEZ, SUPT6H, PPP1R3A, RASSF9, RASSF10, NTRK1, DPYSL2, HDAC1, HDAC6, HDAC3, NINL, CAPZA2, DBN1, FLNA, MYH9, MYO1C, IQGAP1, MATR3, MTX2, SYNPO, ASF1A, LIMA1, ANLN, MYO5C, MYO19, PARD6B, MYO18A, AR, MDM2, SKP2, SNW1, UBXN2B, UBXN2A, LATS1, PARD3, NFATC2, PTPN7, GSK3A, LEO1, PFDN2, PFDN6, RPL13, TERF2, PPP1R16B, SH2D4A, SFRP2, SFRP5, PAK1, PQBP1, PACS1, HSPA1L, DCAF7, MAPRE2, MAPRE1, PPP2R5C, PPP2R5D, DLD, HSD17B10, TRIM25, TES, NR3C2


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 CLCF1_PPP1CA


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 CLCF1_PPP1CA


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCLCF1C1853198COLD-INDUCED SWEATING SYNDROME 21UNIPROT