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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:VAMP4-MYRFL (FusionGDB2 ID:97863)

Fusion Gene Summary for VAMP4-MYRFL

check button Fusion gene summary
Fusion gene informationFusion gene name: VAMP4-MYRFL
Fusion gene ID: 97863
HgeneTgene
Gene symbol

VAMP4

MYRFL

Gene ID

8674

196446

Gene namevesicle associated membrane protein 4myelin regulatory factor like
SynonymsVAMP-4|VAMP24C12orf15|C12orf28|bcm1377
Cytomap

1q24.3

12q15

Type of geneprotein-codingprotein-coding
Descriptionvesicle-associated membrane protein 4VAMP4/TAF3 fusionmyelin regulatory factor-like protein
Modification date2020031320200322
UniProtAcc.

Q96LU7

Ensembl transtripts involved in fusion geneENST00000236192, ENST00000367740, 
ENST00000415773, ENST00000482519, 
ENST00000299350, ENST00000535034, 
ENST00000547771, ENST00000552032, 
Fusion gene scores* DoF score1 X 1 X 1=129 X 16 X 7=3248
# samples 126
** MAII scorelog2(1/1*10)=3.32192809488736log2(26/3248*10)=-3.64296810415672
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: VAMP4 [Title/Abstract] AND MYRFL [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointVAMP4(171707489)-MYRFL(70320351), # samples:1
Anticipated loss of major functional domain due to fusion event.VAMP4-MYRFL seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
VAMP4-MYRFL seems lost the major protein functional domain in Tgene partner, which is a transcription factor 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
HgeneVAMP4

GO:0035493

SNARE complex assembly

21151919


check buttonFusion gene breakpoints across VAMP4 (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 MYRFL (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4SARCTCGA-FX-A2QS-01AVAMP4chr1

171707489

-MYRFLchr12

70320351

+


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Fusion Gene ORF analysis for VAMP4-MYRFL

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-intronENST00000236192ENST00000299350VAMP4chr1

171707489

-MYRFLchr12

70320351

+
5CDS-intronENST00000236192ENST00000535034VAMP4chr1

171707489

-MYRFLchr12

70320351

+
5CDS-intronENST00000367740ENST00000299350VAMP4chr1

171707489

-MYRFLchr12

70320351

+
5CDS-intronENST00000367740ENST00000535034VAMP4chr1

171707489

-MYRFLchr12

70320351

+
5CDS-intronENST00000415773ENST00000299350VAMP4chr1

171707489

-MYRFLchr12

70320351

+
5CDS-intronENST00000415773ENST00000535034VAMP4chr1

171707489

-MYRFLchr12

70320351

+
5UTR-3CDSENST00000482519ENST00000547771VAMP4chr1

171707489

-MYRFLchr12

70320351

+
5UTR-3CDSENST00000482519ENST00000552032VAMP4chr1

171707489

-MYRFLchr12

70320351

+
5UTR-intronENST00000482519ENST00000299350VAMP4chr1

171707489

-MYRFLchr12

70320351

+
5UTR-intronENST00000482519ENST00000535034VAMP4chr1

171707489

-MYRFLchr12

70320351

+
Frame-shiftENST00000236192ENST00000547771VAMP4chr1

171707489

-MYRFLchr12

70320351

+
Frame-shiftENST00000236192ENST00000552032VAMP4chr1

171707489

-MYRFLchr12

70320351

+
Frame-shiftENST00000367740ENST00000547771VAMP4chr1

171707489

-MYRFLchr12

70320351

+
Frame-shiftENST00000367740ENST00000552032VAMP4chr1

171707489

-MYRFLchr12

70320351

+
In-frameENST00000415773ENST00000547771VAMP4chr1

171707489

-MYRFLchr12

70320351

+
In-frameENST00000415773ENST00000552032VAMP4chr1

171707489

-MYRFLchr12

70320351

+

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)
ENST00000415773VAMP4chr1171707489-ENST00000552032MYRFLchr1270320351+15912681871398403
ENST00000415773VAMP4chr1171707489-ENST00000547771MYRFLchr1270320351+19292681871362391

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
ENST00000415773ENST00000552032VAMP4chr1171707489-MYRFLchr1270320351+0.0049840050.99501604
ENST00000415773ENST00000547771VAMP4chr1171707489-MYRFLchr1270320351+0.0016544630.9983455

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Fusion Genomic Features for VAMP4-MYRFL


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)
VAMP4chr1171707488-MYRFLchr1270320350+5.19E-091
VAMP4chr1171707488-MYRFLchr1270320350+5.19E-091

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.
genomic feature

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.
genomic feature of top 1%

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Fusion Protein Features for VAMP4-MYRFL


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/chr1:171707489/chr12:70320351)
- 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
.MYRFL

Q96LU7

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
TgeneMYRFLchr1:171707489chr12:70320351ENST000005520321225543_575534911.0Coiled coilOntology_term=ECO:0000255
TgeneMYRFLchr1:171707489chr12:70320351ENST000005520321225628_648534911.0TransmembraneHelical

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneVAMP4chr1:171707489chr12:70320351ENST00000236192-2852_11222142.0Domainv-SNARE coiled-coil homology
HgeneVAMP4chr1:171707489chr12:70320351ENST00000367740-2852_11222141.0Domainv-SNARE coiled-coil homology
HgeneVAMP4chr1:171707489chr12:70320351ENST00000415773-2952_11222738.6666666666666Domainv-SNARE coiled-coil homology
HgeneVAMP4chr1:171707489chr12:70320351ENST00000236192-28137_14122142.0Topological domainVesicular
HgeneVAMP4chr1:171707489chr12:70320351ENST00000236192-281_11522142.0Topological domainCytoplasmic
HgeneVAMP4chr1:171707489chr12:70320351ENST00000367740-28137_14122141.0Topological domainVesicular
HgeneVAMP4chr1:171707489chr12:70320351ENST00000367740-281_11522141.0Topological domainCytoplasmic
HgeneVAMP4chr1:171707489chr12:70320351ENST00000415773-29137_14122738.6666666666666Topological domainVesicular
HgeneVAMP4chr1:171707489chr12:70320351ENST00000415773-291_11522738.6666666666666Topological domainCytoplasmic
HgeneVAMP4chr1:171707489chr12:70320351ENST00000236192-28116_13622142.0TransmembraneHelical%3B Anchor for type IV membrane protein
HgeneVAMP4chr1:171707489chr12:70320351ENST00000367740-28116_13622141.0TransmembraneHelical%3B Anchor for type IV membrane protein
HgeneVAMP4chr1:171707489chr12:70320351ENST00000415773-29116_13622738.6666666666666TransmembraneHelical%3B Anchor for type IV membrane protein
TgeneMYRFLchr1:171707489chr12:70320351ENST000005520321225142_405534911.0DNA bindingNDT80
TgeneMYRFLchr1:171707489chr12:70320351ENST000005520321225451_559534911.0DomainPeptidase S74


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Fusion Gene Sequence for VAMP4-MYRFL


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.
>97863_97863_1_VAMP4-MYRFL_VAMP4_chr1_171707489_ENST00000415773_MYRFL_chr12_70320351_ENST00000547771_length(transcript)=1929nt_BP=268nt
GAGCGGAGGCGCTGCTGCGGCGCTGCGGCCGACGCCGGGTCCGCACCAACTGTCTCCCCCTCCCAGCTTCTTACCTCGGCTTCCTACTCC
TTCCCCCGCCCGCCCAGCACCGCCAGCCCGGGAGAGCTGCCGGGAGTTCCCCGGGAGCCTCAGGTGGTGACTATCCTGTTGAGAAGCAAA
AGATACTTTGCAAGTAAAAAATATGCCTCCCAAGTTTAAGCGCCACCTCAATGATGATGATGTCACAGGTTCTGTGAAAAGTGAAAGGGA
CCAGATCTTTATGGAAAATGTAGGTGCAGTGAAGCAACTGTGCAAACTAACTAACAACCTTGAGGAAAGAATAGAAGAGTTAGAAATATG
GAACAGAAAGCTGGCCCGGCTAAAGCGGCTCAGTAGTTGGAAGTCATCAGCCAGTGAAGCAAGCACAATCAGCAAATCTAGCAGAGCCGT
TAGTGCATCTTCTCCAAGAAGGGCCGTTCATAAAAAAAACAACAAGGTTTATTTTTCAGGAAAAAGACAGGCGTGTCCTAATTGGGTTTT
CCAGACCTTGGTTATAACTCTGATTGCTGTGATGGCATTTTGCTTAAAAGATCAAGACCGACGTGTCCCAAATCTCCCTCCAAGCAATAT
CACAAGCTCACAGGAGCCAGCTCTGCTGCCCACAGCCTCCTCCTCAGCACCTAATACATCCCTGGTAACCACACCGGCCTCCTTACAAGT
ACCTGAAATTACTTTCTGTGAAATCCTGCCGTGTCAGGAGACTTATTGCTGCCCCATCCGGGGAATGAAAGAAGTCTCTTCAAGTCCTGT
GCAAAGACAATCTGAGGAGAAGGAATTCCATCAGAGGCGATGGTCAGACAAAAGCAAATCAGTTTTGGCAAGAAATGCACTCAGCGGCCC
TGACTGGGAGAGTGACTGGATTGATACAACCATCAGTTCTATTCAGATTATGGAAATCCAGCAAATAATAGATCATCAGTATTGCATTCA
AAGCCTCCAGTGCGGATCTGGAAATTATAATTACAATATTCCTGTTAATAAACACACACCCACCAATGTCAAGTTCTCTCTGGAAATAAA
CACAACAGAGCCATTGATAGTCTTCCAGTGCAAATTCACCCTTGGAAATATATGTTTCCATAGTAAAAGGGGAACCAAAGGGCTGGAAAG
CCACAGAGAAATCTCCCAGGAGATGACACAGGGATATCAGCACATTTGGAGCCTCCCTGTAGCCCCATTTTCTGACAGCATGTTCCATTT
CCGTGTAGCTGCACCGGATTTAGCTGACTGTTCAACTGATCCTTATTTTGCTGGGATATTCTTCACCGATTACTTCTTTTACTTCTATCG
ACGCTGTGCCTAATTTGTTCAAGTTTGGGGACTTTACCAAAGAAAAATACTCAGGAATACATTTAACAGAAACGAACATCCTCTTGCAAC
TTCTTTTTTCTTCTTTGTAAAACATTTACGTTTATTGCTGAAGGACTTTTTCAGGCTTTAGCTTCCAACAGTTTTGAGACATTAATGAGG
AGAATAAAATGTTTGCTGAAACTTGAAATAATGTGATGTTTGATTTTGCCATGACTATGAAGAAAACATTTCCTGGAGCAAACAGTTCTG
TTGAATTTAAAAATACTATTATTTCTGGTATTAAGGAAGTTGTGAGCTCAAAATAAGGAGATCTAGCCTCTATTTTGTTTTAATGTATTT
TAAAGCTTTTGAAAAAACCAAAAGGGCCATGTCGACTTCGGCCCACTAAACATAGACTCTTGAGAATGTGTGATATGGTATGTGGAGGAG
ATGTGGGGGGTGGTATCTGATACTGAGCTCACATTTAGGCAAATTGTCCTATGTGTGTGTGTATTGTATAAACACATACACTAGAGTACA

>97863_97863_1_VAMP4-MYRFL_VAMP4_chr1_171707489_ENST00000415773_MYRFL_chr12_70320351_ENST00000547771_length(amino acids)=391AA_BP=27
MQVKNMPPKFKRHLNDDDVTGSVKSERDQIFMENVGAVKQLCKLTNNLEERIEELEIWNRKLARLKRLSSWKSSASEASTISKSSRAVSA
SSPRRAVHKKNNKVYFSGKRQACPNWVFQTLVITLIAVMAFCLKDQDRRVPNLPPSNITSSQEPALLPTASSSAPNTSLVTTPASLQVPE
ITFCEILPCQETYCCPIRGMKEVSSSPVQRQSEEKEFHQRRWSDKSKSVLARNALSGPDWESDWIDTTISSIQIMEIQQIIDHQYCIQSL
QCGSGNYNYNIPVNKHTPTNVKFSLEINTTEPLIVFQCKFTLGNICFHSKRGTKGLESHREISQEMTQGYQHIWSLPVAPFSDSMFHFRV

--------------------------------------------------------------
>97863_97863_2_VAMP4-MYRFL_VAMP4_chr1_171707489_ENST00000415773_MYRFL_chr12_70320351_ENST00000552032_length(transcript)=1591nt_BP=268nt
GAGCGGAGGCGCTGCTGCGGCGCTGCGGCCGACGCCGGGTCCGCACCAACTGTCTCCCCCTCCCAGCTTCTTACCTCGGCTTCCTACTCC
TTCCCCCGCCCGCCCAGCACCGCCAGCCCGGGAGAGCTGCCGGGAGTTCCCCGGGAGCCTCAGGTGGTGACTATCCTGTTGAGAAGCAAA
AGATACTTTGCAAGTAAAAAATATGCCTCCCAAGTTTAAGCGCCACCTCAATGATGATGATGTCACAGGTTCTGTGAAAAGTGAAAGGGA
CCAGATCTTTATGGAAAATGTAGGTGCAGTGAAGCAACTGTGCAAACTAACTAACAACCTTGAGGAAAGAATAGAAGAGTTAGAAATATG
GAACAGAAAGCTGGCCCGGCTAAAGCGGCTCAGTAGTTGGAAGTCATCAGCCAGTGAAGCAAGCACAATCAGCAAATCTAGCAGAGCCGT
TAGTGCATCTTCTCCAAGAAGGGCCGTTCATAAAAAAAACAACAAGGTTTATTTTTCAGGAAAAAGACAGGCGTGTCCTAATTGGGTTTT
CCAGACCTTGGTTATAACTCTGATTGCTGTGATGGCATTTTGTGCTTTGACGATAGTTGCCCTCTATATACTTAGCTTAAAAGATCAAGA
CCGACGTGTCCCAAATCTCCCTCCAAGCAATATCACAAGCTCACAGGAGCCAGCTCTGCTGCCCACAGCCTCCTCCTCAGCACCTAATAC
ATCCCTGGTAACCACACCGGCCTCCTTACAAGTACCTGAAATTACTTTCTGTGAAATCCTGCCGTGTCAGGAGACTTATTGCTGCCCCAT
CCGGGGAATGAAAGAAGTCTCTTCAAGTCCTGTGCAAAGACAATCTGAGGAGAAGGAATTCCATCAGAGGCGATGGTCAGAAGACAAAAG
CAAATCAGTTTTGGCAAGAAATGCACTCAGCGGCCCTGACTGGGAGAGTGACTGGATTGATACAACCATCAGTTCTATTCAGATTATGGA
AATCCAGCAAATAATAGATCATCAGTATTGCATTCAAAGCCTCCAGTGCGGATCTGGAAATTATAATTACAATATTCCTGTTAATAAACA
CACACCCACCAATGTCAAGTTCTCTCTGGAAATAAACACAACAGAGCCATTGATAGTCTTCCAGTGCAAATTCACCCTTGGAAATATATG
TTTCCATAGTAAAAGGGGAACCAAAGGGCTGGAAAGCCACAGAGAAATCTCCCAGGAGATGACACAGGGATATCAGCACATTTGGAGCCT
CCCTGTAGCCCCATTTTCTGACAGCATGTTCCATTTCCGTGTAGCTGCACCGGATTTAGCTGACTGTTCAACTGATCCTTATTTTGCTGG
GATATTCTTCACCGATTACTTCTTTTACTTCTATCGACGCTGTGCCTAATTTGTTCAAGTTTGGGGACTTTACCAAAGAAAAATACTCAG
GAATACATTTAACAGAAACGAACATCCTCTTGCAACTTCTTTTTTCTTCTTTGTAAAACATTTACGTTTATTGCTGAAGGACTTTTTCAG

>97863_97863_2_VAMP4-MYRFL_VAMP4_chr1_171707489_ENST00000415773_MYRFL_chr12_70320351_ENST00000552032_length(amino acids)=403AA_BP=27
MQVKNMPPKFKRHLNDDDVTGSVKSERDQIFMENVGAVKQLCKLTNNLEERIEELEIWNRKLARLKRLSSWKSSASEASTISKSSRAVSA
SSPRRAVHKKNNKVYFSGKRQACPNWVFQTLVITLIAVMAFCALTIVALYILSLKDQDRRVPNLPPSNITSSQEPALLPTASSSAPNTSL
VTTPASLQVPEITFCEILPCQETYCCPIRGMKEVSSSPVQRQSEEKEFHQRRWSEDKSKSVLARNALSGPDWESDWIDTTISSIQIMEIQ
QIIDHQYCIQSLQCGSGNYNYNIPVNKHTPTNVKFSLEINTTEPLIVFQCKFTLGNICFHSKRGTKGLESHREISQEMTQGYQHIWSLPV

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Fusion Gene PPI Analysis for VAMP4-MYRFL


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 VAMP4-MYRFL


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 VAMP4-MYRFL


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