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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:APC-SYTL4 (FusionGDB2 ID:HG324TG94121)

Fusion Gene Summary for APC-SYTL4

check button Fusion gene summary
Fusion gene informationFusion gene name: APC-SYTL4
Fusion gene ID: hg324tg94121
HgeneTgene
Gene symbol

APC

SYTL4

Gene ID

324

94121

Gene nameAPC regulator of WNT signaling pathwaysynaptotagmin like 4
SynonymsBTPS2|DESMD|DP2|DP2.5|DP3|GS|PPP1R46SLP4
Cytomap('APC')('SYTL4')

5q22.2

Xq22.1

Type of geneprotein-codingprotein-coding
Descriptionadenomatous polyposis coli proteinAPC, WNT signaling pathway regulatorWNT signaling pathway regulatoradenomatosis polyposis coli tumor suppressoradenomatous polyposis coli (APC)deleted in polyposis 2.5epididymis secretory sperm binding proteinprotesynaptotagmin-like protein 4exophilin-2granuphilin-a
Modification date2020032920200322
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000257430, ENST00000457016, 
ENST00000508376, ENST00000505350, 
Fusion gene scores* DoF score14 X 10 X 8=11203 X 3 X 1=9
# samples 143
** MAII scorelog2(14/1120*10)=-3
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/9*10)=1.73696559416621
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: APC [Title/Abstract] AND SYTL4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointAPC(112181077)-SYTL4(99980976), # 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
HgeneAPC

GO:0006974

cellular response to DNA damage stimulus

14728717

HgeneAPC

GO:0007026

negative regulation of microtubule depolymerization

11166179

HgeneAPC

GO:0007050

cell cycle arrest

8521819

HgeneAPC

GO:0008285

negative regulation of cell proliferation

8521819

HgeneAPC

GO:0045736

negative regulation of cyclin-dependent protein serine/threonine kinase activity

8521819

HgeneAPC

GO:0065003

protein-containing complex assembly

16188939

TgeneSYTL4

GO:0001778

plasma membrane repair

27325790



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
ChiTaRS5.0N/ABQ346429APCchr5

112181077

+SYTL4chrX

99980976

-


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Fusion Gene ORF analysis for APC-SYTL4

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
3UTR-intronENST00000257430ENST00000263033APCchr5

112181077

+SYTL4chrX

99980976

-
3UTR-intronENST00000257430ENST00000276141APCchr5

112181077

+SYTL4chrX

99980976

-
3UTR-intronENST00000257430ENST00000372981APCchr5

112181077

+SYTL4chrX

99980976

-
3UTR-intronENST00000257430ENST00000372989APCchr5

112181077

+SYTL4chrX

99980976

-
3UTR-intronENST00000257430ENST00000454200APCchr5

112181077

+SYTL4chrX

99980976

-
3UTR-intronENST00000257430ENST00000455616APCchr5

112181077

+SYTL4chrX

99980976

-
3UTR-intronENST00000257430ENST00000491602APCchr5

112181077

+SYTL4chrX

99980976

-
3UTR-intronENST00000457016ENST00000263033APCchr5

112181077

+SYTL4chrX

99980976

-
3UTR-intronENST00000457016ENST00000276141APCchr5

112181077

+SYTL4chrX

99980976

-
3UTR-intronENST00000457016ENST00000372981APCchr5

112181077

+SYTL4chrX

99980976

-
3UTR-intronENST00000457016ENST00000372989APCchr5

112181077

+SYTL4chrX

99980976

-
3UTR-intronENST00000457016ENST00000454200APCchr5

112181077

+SYTL4chrX

99980976

-
3UTR-intronENST00000457016ENST00000455616APCchr5

112181077

+SYTL4chrX

99980976

-
3UTR-intronENST00000457016ENST00000491602APCchr5

112181077

+SYTL4chrX

99980976

-
3UTR-intronENST00000508376ENST00000263033APCchr5

112181077

+SYTL4chrX

99980976

-
3UTR-intronENST00000508376ENST00000276141APCchr5

112181077

+SYTL4chrX

99980976

-
3UTR-intronENST00000508376ENST00000372981APCchr5

112181077

+SYTL4chrX

99980976

-
3UTR-intronENST00000508376ENST00000372989APCchr5

112181077

+SYTL4chrX

99980976

-
3UTR-intronENST00000508376ENST00000454200APCchr5

112181077

+SYTL4chrX

99980976

-
3UTR-intronENST00000508376ENST00000455616APCchr5

112181077

+SYTL4chrX

99980976

-
3UTR-intronENST00000508376ENST00000491602APCchr5

112181077

+SYTL4chrX

99980976

-
intron-intronENST00000505350ENST00000263033APCchr5

112181077

+SYTL4chrX

99980976

-
intron-intronENST00000505350ENST00000276141APCchr5

112181077

+SYTL4chrX

99980976

-
intron-intronENST00000505350ENST00000372981APCchr5

112181077

+SYTL4chrX

99980976

-
intron-intronENST00000505350ENST00000372989APCchr5

112181077

+SYTL4chrX

99980976

-
intron-intronENST00000505350ENST00000454200APCchr5

112181077

+SYTL4chrX

99980976

-
intron-intronENST00000505350ENST00000455616APCchr5

112181077

+SYTL4chrX

99980976

-
intron-intronENST00000505350ENST00000491602APCchr5

112181077

+SYTL4chrX

99980976

-

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 APC-SYTL4


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 APC-SYTL4


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/:112181077/:99980976)
- 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: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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 APC-SYTL4


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 APC-SYTL4


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 APC-SYTL4


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 APC-SYTL4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneAPCC0032580Adenomatous Polyposis Coli24CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneAPCC2713442Polyposis, Adenomatous Intestinal11CTD_human
HgeneAPCC2713443Familial Intestinal Polyposis11CTD_human
HgeneAPCC0007102Malignant tumor of colon7CTD_human
HgeneAPCC0009375Colonic Neoplasms7CTD_human
HgeneAPCC0009402Colorectal Carcinoma7CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneAPCC0009404Colorectal Neoplasms7CTD_human;UNIPROT
HgeneAPCC0021841Intestinal Neoplasms6CTD_human
HgeneAPCC0346627Intestinal Cancer6CTD_human
HgeneAPCC0001430Adenoma5CTD_human
HgeneAPCC0205646Adenoma, Basal Cell5CTD_human
HgeneAPCC0205647Follicular adenoma5CTD_human
HgeneAPCC0205648Adenoma, Microcystic5CTD_human
HgeneAPCC0205649Adenoma, Monomorphic5CTD_human
HgeneAPCC0205650Papillary adenoma5CTD_human
HgeneAPCC0205651Adenoma, Trabecular5CTD_human
HgeneAPCC0021846Intestinal Polyps3CTD_human
HgeneAPCC0001418Adenocarcinoma2CTD_human
HgeneAPCC0004352Autistic Disorder2CTD_human
HgeneAPCC0007113Rectal Carcinoma2CTD_human
HgeneAPCC0007621Neoplastic Cell Transformation2CTD_human
HgeneAPCC0025149Medulloblastoma2CTD_human;UNIPROT
HgeneAPCC0033578Prostatic Neoplasms2CTD_human
HgeneAPCC0034885Rectal Neoplasms2CTD_human
HgeneAPCC0205641Adenocarcinoma, Basal Cell2CTD_human
HgeneAPCC0205642Adenocarcinoma, Oxyphilic2CTD_human
HgeneAPCC0205643Carcinoma, Cribriform2CTD_human
HgeneAPCC0205644Carcinoma, Granular Cell2CTD_human
HgeneAPCC0205645Adenocarcinoma, Tubular2CTD_human
HgeneAPCC0376358Malignant neoplasm of prostate2CTD_human
HgeneAPCC0002886Anemia, Macrocytic1CTD_human
HgeneAPCC0007131Non-Small Cell Lung Carcinoma1CTD_human
HgeneAPCC0009405Hereditary Nonpolyposis Colorectal Neoplasms1CTD_human
HgeneAPCC0015393Eye Abnormalities1CTD_human
HgeneAPCC0017181Gastrointestinal Hemorrhage1CTD_human
HgeneAPCC0017185Gastrointestinal Neoplasms1CTD_human
HgeneAPCC0017636Glioblastoma1CTD_human
HgeneAPCC0018932Hematochezia1CTD_human
HgeneAPCC0020473Hyperlipidemia1CTD_human
HgeneAPCC0020796Profound Mental Retardation1CTD_human
HgeneAPCC0021390Inflammatory Bowel Diseases1CTD_human
HgeneAPCC0023518Leukocytosis1CTD_human
HgeneAPCC0023903Liver neoplasms1CTD_human
HgeneAPCC0024121Lung Neoplasms1CTD_human
HgeneAPCC0024667Animal Mammary Neoplasms1CTD_human
HgeneAPCC0025363Mental Retardation, Psychosocial1CTD_human
HgeneAPCC0025500Mesothelioma1CTD_human
HgeneAPCC0035222Respiratory Distress Syndrome, Adult1CTD_human
HgeneAPCC0036341Schizophrenia1PSYGENET
HgeneAPCC0038002Splenomegaly1CTD_human
HgeneAPCC0079218Fibromatosis, Aggressive1CGI;CTD_human;ORPHANET
HgeneAPCC0151857Pleocytosis1CTD_human
HgeneAPCC0205833Medullomyoblastoma1CTD_human
HgeneAPCC0206646Fibromatosis, Abdominal1CTD_human
HgeneAPCC0206677Adenomatous Polyps1CTD_human
HgeneAPCC0242379Malignant neoplasm of lung1CTD_human
HgeneAPCC0265325Turcot syndrome (disorder)1CTD_human
HgeneAPCC0278510Childhood Medulloblastoma1CTD_human
HgeneAPCC0278876Adult Medulloblastoma1CTD_human
HgeneAPCC0334588Giant Cell Glioblastoma1CTD_human
HgeneAPCC0345904Malignant neoplasm of liver1CTD_human
HgeneAPCC0685938Malignant neoplasm of gastrointestinal tract1CTD_human
HgeneAPCC0751291Desmoplastic Medulloblastoma1CTD_human
HgeneAPCC0917816Mental deficiency1CTD_human
HgeneAPCC1257925Mammary Carcinoma, Animal1CTD_human
HgeneAPCC1275668Melanotic medulloblastoma1CTD_human
HgeneAPCC1333990Hereditary Nonpolyposis Colorectal Cancer1CTD_human
HgeneAPCC1621958Glioblastoma Multiforme1CTD_human
HgeneAPCC1706412Lipidemias1CTD_human
HgeneAPCC1859309Syndactyly Cenani Lenz type1ORPHANET
HgeneAPCC1879526Aberrant Crypt Foci1CTD_human
HgeneAPCC3714756Intellectual Disability1CTD_human
HgeneAPCC4552100Lynch Syndrome1CTD_human