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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:CNN1-CBS (FusionGDB2 ID:HG1264TG875)

Fusion Gene Summary for CNN1-CBS

check button Fusion gene summary
Fusion gene informationFusion gene name: CNN1-CBS
Fusion gene ID: hg1264tg875
HgeneTgene
Gene symbol

CNN1

CBS

Gene ID

1264

875

Gene namecalponin 1cystathionine beta-synthase
SynonymsHEL-S-14|SMCC|Sm-CalpCBSL|HIP4
Cytomap('CNN1')('CBS')

19p13.2

21q22.3

Type of geneprotein-codingprotein-coding
Descriptioncalponin-1basic calponincalponin 1, basic, smooth musclecalponin H1, smooth musclecalponins, basicepididymis secretory protein Li 14cystathionine beta-synthaseCystathionine beta-synthase-like proteinbeta-thionasemethylcysteine synthaseserine sulfhydrase
Modification date2020031320200320
UniProtAcc

P51911

P35520

Ensembl transtripts involved in fusion geneENST00000252456, ENST00000592923, 
ENST00000535659, ENST00000544952, 
ENST00000588468, 
Fusion gene scores* DoF score7 X 5 X 4=14014 X 4 X 9=504
# samples 712
** MAII scorelog2(7/140*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(12/504*10)=-2.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CNN1 [Title/Abstract] AND CBS [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCNN1(11661138)-CBS(44476011), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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
TgeneCBS

GO:0006563

L-serine metabolic process

19010420

TgeneCBS

GO:0006565

L-serine catabolic process

18776696

TgeneCBS

GO:0019344

cysteine biosynthetic process

24416422

TgeneCBS

GO:0019448

L-cysteine catabolic process

15520012

TgeneCBS

GO:0043418

homocysteine catabolic process

18776696|24416422

TgeneCBS

GO:0050667

homocysteine metabolic process

19010420|20031578|23981774

TgeneCBS

GO:0070814

hydrogen sulfide biosynthetic process

15520012|24416422



check button Fusion gene information
* 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
ChimerDB4SARCTCGA-DX-A6BA-01ACNN1chr19

11661138

-CBSchr21

44476011

-


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Fusion Gene ORF analysis for CNN1-CBS

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-intronENST00000252456ENST00000352178CNN1chr19

11661138

-CBSchr21

44476011

-
5CDS-intronENST00000252456ENST00000359624CNN1chr19

11661138

-CBSchr21

44476011

-
5CDS-intronENST00000252456ENST00000398158CNN1chr19

11661138

-CBSchr21

44476011

-
5CDS-intronENST00000252456ENST00000398165CNN1chr19

11661138

-CBSchr21

44476011

-
5CDS-intronENST00000252456ENST00000398168CNN1chr19

11661138

-CBSchr21

44476011

-
5CDS-intronENST00000252456ENST00000470912CNN1chr19

11661138

-CBSchr21

44476011

-
5CDS-intronENST00000252456ENST00000544202CNN1chr19

11661138

-CBSchr21

44476011

-
5CDS-intronENST00000592923ENST00000352178CNN1chr19

11661138

-CBSchr21

44476011

-
5CDS-intronENST00000592923ENST00000359624CNN1chr19

11661138

-CBSchr21

44476011

-
5CDS-intronENST00000592923ENST00000398158CNN1chr19

11661138

-CBSchr21

44476011

-
5CDS-intronENST00000592923ENST00000398165CNN1chr19

11661138

-CBSchr21

44476011

-
5CDS-intronENST00000592923ENST00000398168CNN1chr19

11661138

-CBSchr21

44476011

-
5CDS-intronENST00000592923ENST00000470912CNN1chr19

11661138

-CBSchr21

44476011

-
5CDS-intronENST00000592923ENST00000544202CNN1chr19

11661138

-CBSchr21

44476011

-
intron-intronENST00000535659ENST00000352178CNN1chr19

11661138

-CBSchr21

44476011

-
intron-intronENST00000535659ENST00000359624CNN1chr19

11661138

-CBSchr21

44476011

-
intron-intronENST00000535659ENST00000398158CNN1chr19

11661138

-CBSchr21

44476011

-
intron-intronENST00000535659ENST00000398165CNN1chr19

11661138

-CBSchr21

44476011

-
intron-intronENST00000535659ENST00000398168CNN1chr19

11661138

-CBSchr21

44476011

-
intron-intronENST00000535659ENST00000470912CNN1chr19

11661138

-CBSchr21

44476011

-
intron-intronENST00000535659ENST00000544202CNN1chr19

11661138

-CBSchr21

44476011

-
intron-intronENST00000544952ENST00000352178CNN1chr19

11661138

-CBSchr21

44476011

-
intron-intronENST00000544952ENST00000359624CNN1chr19

11661138

-CBSchr21

44476011

-
intron-intronENST00000544952ENST00000398158CNN1chr19

11661138

-CBSchr21

44476011

-
intron-intronENST00000544952ENST00000398165CNN1chr19

11661138

-CBSchr21

44476011

-
intron-intronENST00000544952ENST00000398168CNN1chr19

11661138

-CBSchr21

44476011

-
intron-intronENST00000544952ENST00000470912CNN1chr19

11661138

-CBSchr21

44476011

-
intron-intronENST00000544952ENST00000544202CNN1chr19

11661138

-CBSchr21

44476011

-
intron-intronENST00000588468ENST00000352178CNN1chr19

11661138

-CBSchr21

44476011

-
intron-intronENST00000588468ENST00000359624CNN1chr19

11661138

-CBSchr21

44476011

-
intron-intronENST00000588468ENST00000398158CNN1chr19

11661138

-CBSchr21

44476011

-
intron-intronENST00000588468ENST00000398165CNN1chr19

11661138

-CBSchr21

44476011

-
intron-intronENST00000588468ENST00000398168CNN1chr19

11661138

-CBSchr21

44476011

-
intron-intronENST00000588468ENST00000470912CNN1chr19

11661138

-CBSchr21

44476011

-
intron-intronENST00000588468ENST00000544202CNN1chr19

11661138

-CBSchr21

44476011

-

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 CNN1-CBS


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)


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Fusion Protein Features for CNN1-CBS


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/:11661138/:44476011)
- 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
CNN1

P51911

CBS

P35520

FUNCTION: Thin filament-associated protein that is implicated in the regulation and modulation of smooth muscle contraction. It is capable of binding to actin, calmodulin and tropomyosin. The interaction of calponin with actin inhibits the actomyosin Mg-ATPase activity (By similarity). {ECO:0000250}.FUNCTION: Hydro-lyase catalyzing the first step of the transsulfuration pathway, where the hydroxyl group of L-serine is displaced by L-homocysteine in a beta-replacement reaction to form L-cystathionine, the precursor of L-cysteine. This catabolic route allows the elimination of L-methionine and the toxic metabolite L-homocysteine (PubMed:23981774, PubMed:20506325, PubMed:23974653). Also involved in the production of hydrogen sulfide, a gasotransmitter with signaling and cytoprotective effects on neurons (By similarity). {ECO:0000250|UniProtKB:P32232, ECO:0000269|PubMed:20506325, ECO:0000269|PubMed:23974653, ECO:0000269|PubMed:23981774}.

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 CNN1-CBS


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 CNN1-CBS


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 CNN1-CBS


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneCBSP35520DB00114Pyridoxal phosphateCofactorSmall moleculeApproved|Investigational|Nutraceutical
TgeneCBSP35520DB00118AdemetionineActivatorSmall moleculeApproved|Investigational|Nutraceutical
TgeneCBSP35520DB00151CysteineSmall moleculeApproved|Nutraceutical

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Related Diseases for CNN1-CBS


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0751202Cystathionine beta-Synthase Deficiency Disease51CLINGEN;CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0598608Hyperhomocysteinemia3CTD_human
TgeneC0005586Bipolar Disorder1PSYGENET
TgeneC0007222Cardiovascular Diseases1CTD_human
TgeneC0011860Diabetes Mellitus, Non-Insulin-Dependent1CTD_human
TgeneC0020538Hypertensive disease1CTD_human
TgeneC0024302Reticulosarcoma1CTD_human
TgeneC0024304Lymphoma, Mixed-Cell1CTD_human
TgeneC0024305Lymphoma, Non-Hodgkin1CTD_human
TgeneC0024306Lymphoma, Undifferentiated1CTD_human
TgeneC0024796Marfan Syndrome1GENOMICS_ENGLAND
TgeneC0025202melanoma1CTD_human
TgeneC0036341Schizophrenia1PSYGENET
TgeneC0079740High Grade Lymphoma (neoplasm)1CTD_human
TgeneC0079741Lymphoma, Intermediate-Grade1CTD_human
TgeneC0079747Low Grade Lymphoma (neoplasm)1CTD_human
TgeneC0079757Diffuse Mixed-Cell Lymphoma1CTD_human
TgeneC0079770Lymphoma, Small Noncleaved-Cell1CTD_human
TgeneC0162429Malnutrition1CTD_human
TgeneC0338715Drug-induced depressive state1PSYGENET
TgeneC3714542Lymphoma, Diffuse1CTD_human
TgeneC4721532Lymphoma, Non-Hodgkin, Familial1CTD_human