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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:CGNL1-TCF12 (FusionGDB2 ID:16223)

Fusion Gene Summary for CGNL1-TCF12

check button Fusion gene summary
Fusion gene informationFusion gene name: CGNL1-TCF12
Fusion gene ID: 16223
HgeneTgene
Gene symbol

CGNL1

TCF12

Gene ID

84952

6938

Gene namecingulin like 1transcription factor 12
SynonymsJACOP|PCINGCRS3|HEB|HTF4|HsT17266|TCF-12|bHLHb20|p64
Cytomap

15q21.3

15q21.3

Type of geneprotein-codingprotein-coding
Descriptioncingulin-like protein 1junction-associated coiled-coil proteinparacingulintranscription factor 12DNA-binding protein HTF4E-box-binding proteinclass B basic helix-loop-helix protein 20helix-loop-helix transcription factor 4transcription factor HTF-4
Modification date2020031320200313
UniProtAcc

Q0VF96

.
Ensembl transtripts involved in fusion geneENST00000281282, ENST00000557813, 
ENST00000438423, ENST00000267811, 
ENST00000452095, ENST00000333725, 
ENST00000557843, ENST00000560764, 
ENST00000543579, ENST00000537840, 
ENST00000343827, ENST00000559710, 
ENST00000559703, 
Fusion gene scores* DoF score14 X 12 X 3=50421 X 22 X 8=3696
# samples 1626
** MAII scorelog2(16/504*10)=-1.65535182861255
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(26/3696*10)=-3.8293812283876
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CGNL1 [Title/Abstract] AND TCF12 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCGNL1(57754090)-TCF12(57578355), # samples:2
Anticipated loss of major functional domain due to fusion event.CGNL1-TCF12 seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF.
CGNL1-TCF12 seems lost the major protein functional domain in Tgene partner, which is a CGC 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
TgeneTCF12

GO:0045944

positive regulation of transcription by RNA polymerase II

11802795


check buttonFusion gene breakpoints across CGNL1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across TCF12 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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
ChimerDB4BRCATCGA-AR-A251CGNL1chr15

57754090

+TCF12chr15

57578354

+
ChimerDB4BRCATCGA-B6-A0X1-01ACGNL1chr15

57836795

+TCF12chr15

57574643

+
ChimerDB4BRCATCGA-AR-A251-01ACGNL1chr15

57754090

+TCF12chr15

57578355

+
ChimerDB4BRCATCGA-AR-A251-01ACGNL1chr15

57754090

-TCF12chr15

57578355

+


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Fusion Gene ORF analysis for CGNL1-TCF12

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-3UTRENST00000281282ENST00000438423CGNL1chr15

57754090

+TCF12chr15

57578354

+
5CDS-3UTRENST00000281282ENST00000267811CGNL1chr15

57754090

+TCF12chr15

57578354

+
5CDS-3UTRENST00000281282ENST00000452095CGNL1chr15

57754090

+TCF12chr15

57578354

+
5CDS-3UTRENST00000281282ENST00000333725CGNL1chr15

57754090

+TCF12chr15

57578354

+
5CDS-3UTRENST00000281282ENST00000557843CGNL1chr15

57754090

+TCF12chr15

57578354

+
5CDS-intronENST00000281282ENST00000560764CGNL1chr15

57754090

+TCF12chr15

57578354

+
5CDS-3UTRENST00000281282ENST00000543579CGNL1chr15

57754090

+TCF12chr15

57578354

+
5CDS-3UTRENST00000281282ENST00000537840CGNL1chr15

57754090

+TCF12chr15

57578354

+
5CDS-3UTRENST00000281282ENST00000343827CGNL1chr15

57754090

+TCF12chr15

57578354

+
5CDS-3UTRENST00000281282ENST00000559710CGNL1chr15

57754090

+TCF12chr15

57578354

+
5CDS-3UTRENST00000281282ENST00000559703CGNL1chr15

57754090

+TCF12chr15

57578354

+
intron-3UTRENST00000557813ENST00000438423CGNL1chr15

57754090

+TCF12chr15

57578354

+
intron-3UTRENST00000557813ENST00000267811CGNL1chr15

57754090

+TCF12chr15

57578354

+
intron-3UTRENST00000557813ENST00000452095CGNL1chr15

57754090

+TCF12chr15

57578354

+
intron-3UTRENST00000557813ENST00000333725CGNL1chr15

57754090

+TCF12chr15

57578354

+
intron-3UTRENST00000557813ENST00000557843CGNL1chr15

57754090

+TCF12chr15

57578354

+
intron-intronENST00000557813ENST00000560764CGNL1chr15

57754090

+TCF12chr15

57578354

+
intron-3UTRENST00000557813ENST00000543579CGNL1chr15

57754090

+TCF12chr15

57578354

+
intron-3UTRENST00000557813ENST00000537840CGNL1chr15

57754090

+TCF12chr15

57578354

+
intron-3UTRENST00000557813ENST00000343827CGNL1chr15

57754090

+TCF12chr15

57578354

+
intron-3UTRENST00000557813ENST00000559710CGNL1chr15

57754090

+TCF12chr15

57578354

+
intron-3UTRENST00000557813ENST00000559703CGNL1chr15

57754090

+TCF12chr15

57578354

+
Frame-shiftENST00000281282ENST00000438423CGNL1chr15

57836795

+TCF12chr15

57574643

+
Frame-shiftENST00000281282ENST00000267811CGNL1chr15

57836795

+TCF12chr15

57574643

+
Frame-shiftENST00000281282ENST00000452095CGNL1chr15

57836795

+TCF12chr15

57574643

+
Frame-shiftENST00000281282ENST00000333725CGNL1chr15

57836795

+TCF12chr15

57574643

+
Frame-shiftENST00000281282ENST00000557843CGNL1chr15

57836795

+TCF12chr15

57574643

+
5CDS-intronENST00000281282ENST00000560764CGNL1chr15

57836795

+TCF12chr15

57574643

+
5CDS-intronENST00000281282ENST00000543579CGNL1chr15

57836795

+TCF12chr15

57574643

+
5CDS-intronENST00000281282ENST00000537840CGNL1chr15

57836795

+TCF12chr15

57574643

+
5CDS-intronENST00000281282ENST00000343827CGNL1chr15

57836795

+TCF12chr15

57574643

+
5CDS-intronENST00000281282ENST00000559710CGNL1chr15

57836795

+TCF12chr15

57574643

+
5CDS-intronENST00000281282ENST00000559703CGNL1chr15

57836795

+TCF12chr15

57574643

+
intron-3CDSENST00000557813ENST00000438423CGNL1chr15

57836795

+TCF12chr15

57574643

+
intron-3CDSENST00000557813ENST00000267811CGNL1chr15

57836795

+TCF12chr15

57574643

+
intron-3CDSENST00000557813ENST00000452095CGNL1chr15

57836795

+TCF12chr15

57574643

+
intron-3CDSENST00000557813ENST00000333725CGNL1chr15

57836795

+TCF12chr15

57574643

+
intron-3CDSENST00000557813ENST00000557843CGNL1chr15

57836795

+TCF12chr15

57574643

+
intron-intronENST00000557813ENST00000560764CGNL1chr15

57836795

+TCF12chr15

57574643

+
intron-intronENST00000557813ENST00000543579CGNL1chr15

57836795

+TCF12chr15

57574643

+
intron-intronENST00000557813ENST00000537840CGNL1chr15

57836795

+TCF12chr15

57574643

+
intron-intronENST00000557813ENST00000343827CGNL1chr15

57836795

+TCF12chr15

57574643

+
intron-intronENST00000557813ENST00000559710CGNL1chr15

57836795

+TCF12chr15

57574643

+
intron-intronENST00000557813ENST00000559703CGNL1chr15

57836795

+TCF12chr15

57574643

+
5CDS-3UTRENST00000281282ENST00000438423CGNL1chr15

57754090

+TCF12chr15

57578355

+
5CDS-3UTRENST00000281282ENST00000267811CGNL1chr15

57754090

+TCF12chr15

57578355

+
5CDS-3UTRENST00000281282ENST00000452095CGNL1chr15

57754090

+TCF12chr15

57578355

+
5CDS-3UTRENST00000281282ENST00000333725CGNL1chr15

57754090

+TCF12chr15

57578355

+
5CDS-3UTRENST00000281282ENST00000557843CGNL1chr15

57754090

+TCF12chr15

57578355

+
5CDS-intronENST00000281282ENST00000560764CGNL1chr15

57754090

+TCF12chr15

57578355

+
5CDS-3UTRENST00000281282ENST00000543579CGNL1chr15

57754090

+TCF12chr15

57578355

+
5CDS-3UTRENST00000281282ENST00000537840CGNL1chr15

57754090

+TCF12chr15

57578355

+
5CDS-3UTRENST00000281282ENST00000343827CGNL1chr15

57754090

+TCF12chr15

57578355

+
5CDS-3UTRENST00000281282ENST00000559710CGNL1chr15

57754090

+TCF12chr15

57578355

+
5CDS-3UTRENST00000281282ENST00000559703CGNL1chr15

57754090

+TCF12chr15

57578355

+
intron-3UTRENST00000557813ENST00000438423CGNL1chr15

57754090

+TCF12chr15

57578355

+
intron-3UTRENST00000557813ENST00000267811CGNL1chr15

57754090

+TCF12chr15

57578355

+
intron-3UTRENST00000557813ENST00000452095CGNL1chr15

57754090

+TCF12chr15

57578355

+
intron-3UTRENST00000557813ENST00000333725CGNL1chr15

57754090

+TCF12chr15

57578355

+
intron-3UTRENST00000557813ENST00000557843CGNL1chr15

57754090

+TCF12chr15

57578355

+
intron-intronENST00000557813ENST00000560764CGNL1chr15

57754090

+TCF12chr15

57578355

+
intron-3UTRENST00000557813ENST00000543579CGNL1chr15

57754090

+TCF12chr15

57578355

+
intron-3UTRENST00000557813ENST00000537840CGNL1chr15

57754090

+TCF12chr15

57578355

+
intron-3UTRENST00000557813ENST00000343827CGNL1chr15

57754090

+TCF12chr15

57578355

+
intron-3UTRENST00000557813ENST00000559710CGNL1chr15

57754090

+TCF12chr15

57578355

+
intron-3UTRENST00000557813ENST00000559703CGNL1chr15

57754090

+TCF12chr15

57578355

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

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

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Fusion Genomic Features for CGNL1-TCF12


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)
CGNL1chr1557836795+TCF12chr1557574642+0.0008196780.99918026
CGNL1chr1557754090+TCF12chr1557578354+3.29E-060.99999666
CGNL1chr1557754090+TCF12chr1557578354+3.29E-060.99999666
CGNL1chr1557836795+TCF12chr1557574642+0.0008196780.99918026
CGNL1chr1557754090+TCF12chr1557578354+3.29E-060.99999666
CGNL1chr1557754090+TCF12chr1557578354+3.29E-060.99999666

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for CGNL1-TCF12


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
CGNL1

Q0VF96

.
FUNCTION: May be involved in anchoring the apical junctional complex, especially tight junctions, to actin-based cytoskeletons. {ECO:0000269|PubMed:22891260}.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.
- 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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Fusion Gene Sequence for CGNL1-TCF12


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for CGNL1-TCF12


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


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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Related Drugs for CGNL1-TCF12


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for CGNL1-TCF12


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCGNL1C0036341Schizophrenia1PSYGENET
TgeneTCF12C3715051CRANIOSYNOSTOSIS 33GENOMICS_ENGLAND;UNIPROT
TgeneTCF12C0010278Craniosynostosis1CTD_human
TgeneTCF12C0030044Acrocephaly1CTD_human
TgeneTCF12C0221356Brachycephaly1CTD_human;ORPHANET
TgeneTCF12C0265529Plagiocephaly1ORPHANET
TgeneTCF12C0265534Scaphycephaly1CTD_human
TgeneTCF12C0265535Trigonocephaly1CTD_human
TgeneTCF12C1275278Extraskeletal Myxoid Chondrosarcoma1ORPHANET
TgeneTCF12C1833340Synostotic Posterior Plagiocephaly1CTD_human
TgeneTCF12C1856266Coronal craniosynostosis1GENOMICS_ENGLAND
TgeneTCF12C1860819Metopic synostosis1CTD_human
TgeneTCF12C2931150Synostotic Anterior Plagiocephaly1CTD_human
TgeneTCF12C4551902Craniosynostosis, Type 11CTD_human