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Center for Computational Systems Medicine level2
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein Structure

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pLDDT scores

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Ramachandran Plot of Fusion Protein Structure

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:PPP3CA-INTS12

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PPP3CA-INTS12
FusionPDB ID: 68119
FusionGDB2.0 ID: 68119
HgeneTgene
Gene symbol

PPP3CA

INTS12

Gene ID

5530

57117

Gene nameprotein phosphatase 3 catalytic subunit alphaintegrator complex subunit 12
SynonymsACCIID|CALN|CALNA|CALNA1|CCN1|CNA1|IECEE|IECEE1|PPP2BINT12|PHF22|SBBI22
Cytomap

4q24

4q24

Type of geneprotein-codingprotein-coding
Descriptionserine/threonine-protein phosphatase 2B catalytic subunit alpha isoformCAM-PRP catalytic subunitcalcineurin A alphacalmodulin-dependent calcineurin A subunit alpha isoformprotein phosphatase 2B, catalytic subunit, alpha isoformprotein phosphatase 3 (integrator complex subunit 12PHD finger protein 22hypothetical nuclear factor SBBI22
Modification date2020031520200313
UniProtAcc.

Q96CB8

Ensembl transtripts involved in fusion geneENST idsENST00000323055, ENST00000394853, 
ENST00000394854, ENST00000512215, 
ENST00000507176, ENST00000510292, 
ENST00000523694, 
ENST00000451321, 
ENST00000340139, ENST00000394735, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score25 X 13 X 8=26003 X 2 X 2=12
# samples 232
** MAII scorelog2(23/2600*10)=-3.49880585697144
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(2/12*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)

PubMed: PPP3CA [Title/Abstract] AND INTS12 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PPP3CA(102117073)-INTS12(106604474), # samples:3
Anticipated loss of major functional domain due to fusion event.PPP3CA-INTS12 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
PPP3CA-INTS12 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
PPP3CA-INTS12 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
PPP3CA-INTS12 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
PPP3CA-INTS12 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
* 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
HgenePPP3CA

GO:0006470

protein dephosphorylation

18815128|19154138

HgenePPP3CA

GO:0033173

calcineurin-NFAT signaling cascade

19154138|22688515

HgenePPP3CA

GO:0035690

cellular response to drug

11005320

HgenePPP3CA

GO:0045944

positive regulation of transcription by RNA polymerase II

22688515

HgenePPP3CA

GO:0051592

response to calcium ion

18815128

TgeneINTS12

GO:0016180

snRNA processing

16239144


check buttonFusion gene breakpoints across PPP3CA (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across INTS12 (3'-gene)
* 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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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4PRADTCGA-HC-8266-01APPP3CAchr4

102117073

-INTS12chr4

106604474

-
ChimerDB4PRADTCGA-HC-8266PPP3CAchr4

102117073

-INTS12chr4

106604474

-


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000512215PPP3CAchr4102117073-ENST00000394735INTS12chr4106604474-16319401550888220
ENST00000512215PPP3CAchr4102117073-ENST00000340139INTS12chr4106604474-16319401550888220
ENST00000394854PPP3CAchr4102117073-ENST00000394735INTS12chr4106604474-16349431553891220
ENST00000394854PPP3CAchr4102117073-ENST00000340139INTS12chr4106604474-16349431553891220
ENST00000323055PPP3CAchr4102117073-ENST00000394735INTS12chr4106604474-16259341544882220
ENST00000323055PPP3CAchr4102117073-ENST00000340139INTS12chr4106604474-16259341544882220
ENST00000394853PPP3CAchr4102117073-ENST00000394735INTS12chr4106604474-14817901400738220
ENST00000394853PPP3CAchr4102117073-ENST00000340139INTS12chr4106604474-14817901400738220

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score
ENST00000512215ENST00000394735PPP3CAchr4102117073-INTS12chr4106604474-0.0248509650.975149
ENST00000512215ENST00000340139PPP3CAchr4102117073-INTS12chr4106604474-0.0248509650.975149
ENST00000394854ENST00000394735PPP3CAchr4102117073-INTS12chr4106604474-0.0275335960.9724664
ENST00000394854ENST00000340139PPP3CAchr4102117073-INTS12chr4106604474-0.0275335960.9724664
ENST00000323055ENST00000394735PPP3CAchr4102117073-INTS12chr4106604474-0.021411340.9785887
ENST00000323055ENST00000340139PPP3CAchr4102117073-INTS12chr4106604474-0.021411340.9785887
ENST00000394853ENST00000394735PPP3CAchr4102117073-INTS12chr4106604474-0.0276355560.97236437
ENST00000394853ENST00000340139PPP3CAchr4102117073-INTS12chr4106604474-0.0276355560.97236437

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>68119_68119_1_PPP3CA-INTS12_PPP3CA_chr4_102117073_ENST00000323055_INTS12_chr4_106604474_ENST00000340139_length(amino acids)=220AA_BP=0
MIQKPTWPHYFLSFFWAAFFLTICNRFIALSCDSCEVGPLRDAEGELLDSEVVLLVVLPLGPDVPLFPFPLSWLLLPGTKLLGLGRPTLL
TLSQLTERLRPVLPKVRGGGGFKGTVGVVLLLEPILEPIPPLDDVARPVKPTGFWLADEVAGFPVLFCVVELNFAVEGPAEEVLAAKAAH

--------------------------------------------------------------

>68119_68119_2_PPP3CA-INTS12_PPP3CA_chr4_102117073_ENST00000323055_INTS12_chr4_106604474_ENST00000394735_length(amino acids)=220AA_BP=0
MIQKPTWPHYFLSFFWAAFFLTICNRFIALSCDSCEVGPLRDAEGELLDSEVVLLVVLPLGPDVPLFPFPLSWLLLPGTKLLGLGRPTLL
TLSQLTERLRPVLPKVRGGGGFKGTVGVVLLLEPILEPIPPLDDVARPVKPTGFWLADEVAGFPVLFCVVELNFAVEGPAEEVLAAKAAH

--------------------------------------------------------------

>68119_68119_3_PPP3CA-INTS12_PPP3CA_chr4_102117073_ENST00000394853_INTS12_chr4_106604474_ENST00000340139_length(amino acids)=220AA_BP=0
MIQKPTWPHYFLSFFWAAFFLTICNRFIALSCDSCEVGPLRDAEGELLDSEVVLLVVLPLGPDVPLFPFPLSWLLLPGTKLLGLGRPTLL
TLSQLTERLRPVLPKVRGGGGFKGTVGVVLLLEPILEPIPPLDDVARPVKPTGFWLADEVAGFPVLFCVVELNFAVEGPAEEVLAAKAAH

--------------------------------------------------------------

>68119_68119_4_PPP3CA-INTS12_PPP3CA_chr4_102117073_ENST00000394853_INTS12_chr4_106604474_ENST00000394735_length(amino acids)=220AA_BP=0
MIQKPTWPHYFLSFFWAAFFLTICNRFIALSCDSCEVGPLRDAEGELLDSEVVLLVVLPLGPDVPLFPFPLSWLLLPGTKLLGLGRPTLL
TLSQLTERLRPVLPKVRGGGGFKGTVGVVLLLEPILEPIPPLDDVARPVKPTGFWLADEVAGFPVLFCVVELNFAVEGPAEEVLAAKAAH

--------------------------------------------------------------

>68119_68119_5_PPP3CA-INTS12_PPP3CA_chr4_102117073_ENST00000394854_INTS12_chr4_106604474_ENST00000340139_length(amino acids)=220AA_BP=0
MIQKPTWPHYFLSFFWAAFFLTICNRFIALSCDSCEVGPLRDAEGELLDSEVVLLVVLPLGPDVPLFPFPLSWLLLPGTKLLGLGRPTLL
TLSQLTERLRPVLPKVRGGGGFKGTVGVVLLLEPILEPIPPLDDVARPVKPTGFWLADEVAGFPVLFCVVELNFAVEGPAEEVLAAKAAH

--------------------------------------------------------------

>68119_68119_6_PPP3CA-INTS12_PPP3CA_chr4_102117073_ENST00000394854_INTS12_chr4_106604474_ENST00000394735_length(amino acids)=220AA_BP=0
MIQKPTWPHYFLSFFWAAFFLTICNRFIALSCDSCEVGPLRDAEGELLDSEVVLLVVLPLGPDVPLFPFPLSWLLLPGTKLLGLGRPTLL
TLSQLTERLRPVLPKVRGGGGFKGTVGVVLLLEPILEPIPPLDDVARPVKPTGFWLADEVAGFPVLFCVVELNFAVEGPAEEVLAAKAAH

--------------------------------------------------------------

>68119_68119_7_PPP3CA-INTS12_PPP3CA_chr4_102117073_ENST00000512215_INTS12_chr4_106604474_ENST00000340139_length(amino acids)=220AA_BP=0
MIQKPTWPHYFLSFFWAAFFLTICNRFIALSCDSCEVGPLRDAEGELLDSEVVLLVVLPLGPDVPLFPFPLSWLLLPGTKLLGLGRPTLL
TLSQLTERLRPVLPKVRGGGGFKGTVGVVLLLEPILEPIPPLDDVARPVKPTGFWLADEVAGFPVLFCVVELNFAVEGPAEEVLAAKAAH

--------------------------------------------------------------

>68119_68119_8_PPP3CA-INTS12_PPP3CA_chr4_102117073_ENST00000512215_INTS12_chr4_106604474_ENST00000394735_length(amino acids)=220AA_BP=0
MIQKPTWPHYFLSFFWAAFFLTICNRFIALSCDSCEVGPLRDAEGELLDSEVVLLVVLPLGPDVPLFPFPLSWLLLPGTKLLGLGRPTLL
TLSQLTERLRPVLPKVRGGGGFKGTVGVVLLLEPILEPIPPLDDVARPVKPTGFWLADEVAGFPVLFCVVELNFAVEGPAEEVLAAKAAH

--------------------------------------------------------------

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Fusion Protein Functional Features


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr4:102117073/chr4:106604474)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.INTS12

Q96CB8

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Component of the Integrator complex, a complex involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. The Integrator complex is associated with the C-terminal domain (CTD) of RNA polymerase II largest subunit (POLR2A) and is recruited to the U1 and U2 snRNAs genes (PubMed:16239144). Mediates recruitment of cytoplasmic dynein to the nuclear envelope, probably as component of the INT complex (PubMed:23904267). {ECO:0000269|PubMed:16239144, ECO:0000269|PubMed:23904267}.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneINTS12chr4:102117073chr4:106604474ENST0000034013968270_440268.0463.0Compositional biasNote=Ser-rich
TgeneINTS12chr4:102117073chr4:106604474ENST0000039473568270_440268.0463.0Compositional biasNote=Ser-rich
TgeneINTS12chr4:102117073chr4:106604474ENST0000045132157270_440268.0463.0Compositional biasNote=Ser-rich

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePPP3CAchr4:102117073chr4:106604474ENST00000323055-212307_31186.33333333333333470.0MotifSAPNY motif
HgenePPP3CAchr4:102117073chr4:106604474ENST00000394853-213307_31186.33333333333333512.0MotifSAPNY motif
HgenePPP3CAchr4:102117073chr4:106604474ENST00000394854-214307_31186.33333333333333522.0MotifSAPNY motif
HgenePPP3CAchr4:102117073chr4:106604474ENST00000512215-28307_31186.33333333333333290.0MotifSAPNY motif
HgenePPP3CAchr4:102117073chr4:106604474ENST00000323055-212341_36986.33333333333333470.0RegionCalcineurin B binding
HgenePPP3CAchr4:102117073chr4:106604474ENST00000323055-212392_40686.33333333333333470.0RegionCalmodulin-binding
HgenePPP3CAchr4:102117073chr4:106604474ENST00000323055-212407_41486.33333333333333470.0RegionAutoinhibitory segment
HgenePPP3CAchr4:102117073chr4:106604474ENST00000323055-212465_48786.33333333333333470.0RegionAutoinhibitory domain
HgenePPP3CAchr4:102117073chr4:106604474ENST00000323055-21256_34086.33333333333333470.0RegionCatalytic
HgenePPP3CAchr4:102117073chr4:106604474ENST00000394853-213341_36986.33333333333333512.0RegionCalcineurin B binding
HgenePPP3CAchr4:102117073chr4:106604474ENST00000394853-213392_40686.33333333333333512.0RegionCalmodulin-binding
HgenePPP3CAchr4:102117073chr4:106604474ENST00000394853-213407_41486.33333333333333512.0RegionAutoinhibitory segment
HgenePPP3CAchr4:102117073chr4:106604474ENST00000394853-213465_48786.33333333333333512.0RegionAutoinhibitory domain
HgenePPP3CAchr4:102117073chr4:106604474ENST00000394853-21356_34086.33333333333333512.0RegionCatalytic
HgenePPP3CAchr4:102117073chr4:106604474ENST00000394854-214341_36986.33333333333333522.0RegionCalcineurin B binding
HgenePPP3CAchr4:102117073chr4:106604474ENST00000394854-214392_40686.33333333333333522.0RegionCalmodulin-binding
HgenePPP3CAchr4:102117073chr4:106604474ENST00000394854-214407_41486.33333333333333522.0RegionAutoinhibitory segment
HgenePPP3CAchr4:102117073chr4:106604474ENST00000394854-214465_48786.33333333333333522.0RegionAutoinhibitory domain
HgenePPP3CAchr4:102117073chr4:106604474ENST00000394854-21456_34086.33333333333333522.0RegionCatalytic
HgenePPP3CAchr4:102117073chr4:106604474ENST00000512215-28341_36986.33333333333333290.0RegionCalcineurin B binding
HgenePPP3CAchr4:102117073chr4:106604474ENST00000512215-28392_40686.33333333333333290.0RegionCalmodulin-binding
HgenePPP3CAchr4:102117073chr4:106604474ENST00000512215-28407_41486.33333333333333290.0RegionAutoinhibitory segment
HgenePPP3CAchr4:102117073chr4:106604474ENST00000512215-28465_48786.33333333333333290.0RegionAutoinhibitory domain
HgenePPP3CAchr4:102117073chr4:106604474ENST00000512215-2856_34086.33333333333333290.0RegionCatalytic
TgeneINTS12chr4:102117073chr4:106604474ENST0000034013968159_215268.0463.0Zinc fingerPHD-type
TgeneINTS12chr4:102117073chr4:106604474ENST0000039473568159_215268.0463.0Zinc fingerPHD-type
TgeneINTS12chr4:102117073chr4:106604474ENST0000045132157159_215268.0463.0Zinc fingerPHD-type


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Fusion Protein Structures

check button PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
Fusion protein PDB link (fusion AA seq ID in FusionPDB)HgeneHchrHbpHstrandTgeneTchrTbpTstrandAA seqLen(AA seq)
PDB file >>>327_PPP3CA_102117073_INTS12_106604474_ranked_0.pdbPPP3CA102117073102117073ENST00000340139INTS12chr4106604474-
MIQKPTWPHYFLSFFWAAFFLTICNRFIALSCDSCEVGPLRDAEGELLDSEVVLLVVLPLGPDVPLFPFPLSWLLLPGTKLLGLGRPTLL
TLSQLTERLRPVLPKVRGGGGFKGTVGVVLLLEPILEPIPPLDDVARPVKPTGFWLADEVAGFPVLFCVVELNFAVEGPAEEVLAAKAAH
220


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pLDDT score distribution

check button pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
PPP3CA_pLDDT.png
all structure
all structure
INTS12_pLDDT.png
all structure
all structure

check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
all structure


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Ramachandran Plot of Fusion Protein Structure


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.
Fusion AA seq ID in FusionPDB and their Ramachandran plots

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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
PPP3CA
INTS12


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with
HgenePPP3CAchr4:102117073chr4:106604474ENST00000323055-212327_33686.33333333333333470.0PxIxIF motif in substrate
HgenePPP3CAchr4:102117073chr4:106604474ENST00000394853-213327_33686.33333333333333512.0PxIxIF motif in substrate
HgenePPP3CAchr4:102117073chr4:106604474ENST00000394854-214327_33686.33333333333333522.0PxIxIF motif in substrate
HgenePPP3CAchr4:102117073chr4:106604474ENST00000512215-28327_33686.33333333333333290.0PxIxIF motif in substrate


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Related Drugs to PPP3CA-INTS12


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to PPP3CA-INTS12


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource