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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:SLC12A2-PPP2CA

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SLC12A2-PPP2CA
FusionPDB ID: 82218
FusionGDB2.0 ID: 82218
HgeneTgene
Gene symbol

SLC12A2

PPP2CA

Gene ID

6558

5515

Gene namesolute carrier family 12 member 2protein phosphatase 2 catalytic subunit alpha
SynonymsBSC|BSC2|NKCC1|PPP1R141NEDLBA|PP2Ac|PP2CA|PP2Calpha|RP-C
Cytomap

5q23.3

5q31.1

Type of geneprotein-codingprotein-coding
Descriptionsolute carrier family 12 member 2basolateral Na-K-Cl symporterbumetanide-sensitive sodium-(potassium)-chloride cotransporter 1bumetanide-sensitive sodium-(potassium)-chloride cotransporter 2protein phosphatase 1, regulatory subunit 141solute carrier serine/threonine-protein phosphatase 2A catalytic subunit alpha isoformPP2A-alphaprotein phosphatase 2 (formerly 2A), catalytic subunit, alpha isoformprotein phosphatase 2, catalytic subunit, alpha isozymereplication protein Cserine/threonine protein
Modification date2020032720200315
UniProtAcc..
Ensembl transtripts involved in fusion geneENST idsENST00000262461, ENST00000343225, 
ENST00000507791, 
ENST00000231504, 
ENST00000481195, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score14 X 13 X 4=7288 X 8 X 5=320
# samples 1611
** MAII scorelog2(16/728*10)=-2.18586654531133
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(11/320*10)=-1.5405683813627
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: SLC12A2 [Title/Abstract] AND PPP2CA [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SLC12A2(127420402)-PPP2CA(133537712), # samples:3
Anticipated loss of major functional domain due to fusion event.SLC12A2-PPP2CA 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.
SLC12A2-PPP2CA 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.
* 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
HgeneSLC12A2

GO:0015696

ammonium transport

12946942|18032481

HgeneSLC12A2

GO:0030321

transepithelial chloride transport

12946942

HgeneSLC12A2

GO:0070634

transepithelial ammonium transport

18032481

TgenePPP2CA

GO:0035970

peptidyl-threonine dephosphorylation

30611118


check buttonFusion gene breakpoints across SLC12A2 (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 PPP2CA (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
ChimerDB4STADTCGA-HU-A4GH-01ASLC12A2chr5

127420402

+PPP2CAchr5

133537712

-
ChimerDB4STADTCGA-HU-A4GHSLC12A2chr5

127420402

+PPP2CAchr5

133537712

-


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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)
ENST00000262461SLC12A2chr5127420402+ENST00000481195PPP2CAchr5133537712-5001945331562509
ENST00000343225SLC12A2chr5127420402+ENST00000481195PPP2CAchr5133537712-491986381480490

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
ENST00000262461ENST00000481195SLC12A2chr5127420402+PPP2CAchr5133537712-0.0002261560.9997738
ENST00000343225ENST00000481195SLC12A2chr5127420402+PPP2CAchr5133537712-0.0002047370.99979526

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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

>82218_82218_1_SLC12A2-PPP2CA_SLC12A2_chr5_127420402_ENST00000262461_PPP2CA_chr5_133537712_ENST00000481195_length(amino acids)=509AA_BP=304
MWPSRLAAARRRRGERLSHLVLRLWPPPARGVEGVLPETSAGLCSSAGGRAAMEPRPTAPSSGAPGLAGVGETPSAAALAAARVELPGTA
VPSVPEDAAPASRDGGGVRDEGPAAAGDGLGRPLGPTPSQSRFQVDLVSENAGRAAAAAAAAAAAAAAAGAGAGAKQTPADGEASGESEP
AKGSEEAKGRFRVNFVDPAASSSAEDSLSDAAGVGVDGPNVSFQNGGDTVLSEGSSLHSGGGGGSGHHQHYYYDTHTNTYYLRTFGHNTM
DAVPRIDHYRHTAAQLGEKLLRPSLAELHDELEKVRYRERITILRGNHESRQITQVYGFYDECLRKYGNANVWKYFTDLFDYLPLTALVD
GQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGPMCDLLWSDPDDRGGWGISPRGAGYTFGQDISETFNHANGLTLVSRAHQLVMEGYNW

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>82218_82218_2_SLC12A2-PPP2CA_SLC12A2_chr5_127420402_ENST00000343225_PPP2CA_chr5_133537712_ENST00000481195_length(amino acids)=490AA_BP=285
MVLRLWPPPARGVEGVLPETSAGLCSSAGGRAAMEPRPTAPSSGAPGLAGVGETPSAAALAAARVELPGTAVPSVPEDAAPASRDGGGVR
DEGPAAAGDGLGRPLGPTPSQSRFQVDLVSENAGRAAAAAAAAAAAAAAAGAGAGAKQTPADGEASGESEPAKGSEEAKGRFRVNFVDPA
ASSSAEDSLSDAAGVGVDGPNVSFQNGGDTVLSEGSSLHSGGGGGSGHHQHYYYDTHTNTYYLRTFGHNTMDAVPRIDHYRHTAAQLGEK
LLRPSLAELHDELEKVRYRERITILRGNHESRQITQVYGFYDECLRKYGNANVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDH
IRALDRLQEVPHEGPMCDLLWSDPDDRGGWGISPRGAGYTFGQDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCYRC

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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/chr5:127420402/chr5:133537712)
- 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
..
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: 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.

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
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127188_194252.01213.0Compositional biasNote=Poly-Gly
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+12790_122252.01213.0Compositional biasNote=Ala-rich
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126188_194252.01197.0Compositional biasNote=Poly-Gly
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+12690_122252.01197.0Compositional biasNote=Ala-rich

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127287_299252.01213.0IntramembraneHelical
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127300_307252.01213.0IntramembraneOntology_term=ECO:0000305
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127308_313252.01213.0IntramembraneHelical
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127487_498252.01213.0IntramembraneHelical
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127499_500252.01213.0IntramembraneOntology_term=ECO:0000305
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127501_507252.01213.0IntramembraneHelical
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126287_299252.01197.0IntramembraneHelical
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126300_307252.01197.0IntramembraneOntology_term=ECO:0000305
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126308_313252.01197.0IntramembraneHelical
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126487_498252.01197.0IntramembraneHelical
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126499_500252.01197.0IntramembraneOntology_term=ECO:0000305
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126501_507252.01197.0IntramembraneHelical
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+1271_286252.01213.0Topological domainCytoplasmic
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127314_321252.01213.0Topological domainExtracellular
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127344_361252.01213.0Topological domainCytoplasmic
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127398_406252.01213.0Topological domainExtracellular
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127425_429252.01213.0Topological domainCytoplasmic
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127455_486252.01213.0Topological domainExtracellular
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127508_514252.01213.0Topological domainCytoplasmic
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127543_599252.01213.0Topological domainExtracellular
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127633_653252.01213.0Topological domainCytoplasmic
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127669_670252.01213.0Topological domainExtracellular
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127698_711252.01213.0Topological domainCytoplasmic
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127731_731252.01213.0Topological domainExtracellular
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127752_1212252.01213.0Topological domainCytoplasmic
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+1261_286252.01197.0Topological domainCytoplasmic
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126314_321252.01197.0Topological domainExtracellular
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126344_361252.01197.0Topological domainCytoplasmic
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126398_406252.01197.0Topological domainExtracellular
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126425_429252.01197.0Topological domainCytoplasmic
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126455_486252.01197.0Topological domainExtracellular
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126508_514252.01197.0Topological domainCytoplasmic
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126543_599252.01197.0Topological domainExtracellular
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126633_653252.01197.0Topological domainCytoplasmic
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126669_670252.01197.0Topological domainExtracellular
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126698_711252.01197.0Topological domainCytoplasmic
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126731_731252.01197.0Topological domainExtracellular
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126752_1212252.01197.0Topological domainCytoplasmic
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127287_313252.01213.0TransmembraneDiscontinuously helical
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127322_343252.01213.0TransmembraneHelical
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127407_424252.01213.0TransmembraneHelical
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127430_454252.01213.0TransmembraneHelical
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127487_507252.01213.0TransmembraneDiscontinuously helical
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127515_542252.01213.0TransmembraneHelical
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127600_632252.01213.0TransmembraneHelical
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127654_668252.01213.0TransmembraneHelical
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000262461+127712_730252.01213.0TransmembraneHelical
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126287_313252.01197.0TransmembraneDiscontinuously helical
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126322_343252.01197.0TransmembraneHelical
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126407_424252.01197.0TransmembraneHelical
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126430_454252.01197.0TransmembraneHelical
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126487_507252.01197.0TransmembraneDiscontinuously helical
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126515_542252.01197.0TransmembraneHelical
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126600_632252.01197.0TransmembraneHelical
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126654_668252.01197.0TransmembraneHelical
HgeneSLC12A2chr5:127420402chr5:133537712ENST00000343225+126712_730252.01197.0TransmembraneHelical


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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 >>>1083_SLC12A2_127420402_PPP2CA_133537712_1083_SLC12A2_127420402_PPP2CA_133537712_ranked_0.pdbSLC12A2127420402127420402ENST00000481195PPP2CAchr5133537712-
MWPSRLAAARRRRGERLSHLVLRLWPPPARGVEGVLPETSAGLCSSAGGRAAMEPRPTAPSSGAPGLAGVGETPSAAALAAARVELPGTA
VPSVPEDAAPASRDGGGVRDEGPAAAGDGLGRPLGPTPSQSRFQVDLVSENAGRAAAAAAAAAAAAAAAGAGAGAKQTPADGEASGESEP
AKGSEEAKGRFRVNFVDPAASSSAEDSLSDAAGVGVDGPNVSFQNGGDTVLSEGSSLHSGGGGGSGHHQHYYYDTHTNTYYLRTFGHNTM
DAVPRIDHYRHTAAQLGEKLLRPSLAELHDELEKVRYRERITILRGNHESRQITQVYGFYDECLRKYGNANVWKYFTDLFDYLPLTALVD
GQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGPMCDLLWSDPDDRGGWGISPRGAGYTFGQDISETFNHANGLTLVSRAHQLVMEGYNW
509


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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.
SLC12A2_pLDDT.png
all structure
all structure
PPP2CA_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
SLC12A2
PPP2CA


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


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Related Drugs to SLC12A2-PPP2CA


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 SLC12A2-PPP2CA


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