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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:FAM118A-VAPB (FusionGDB2 ID:HG55007TG9217)

Fusion Gene Summary for FAM118A-VAPB

check button Fusion gene summary
Fusion gene informationFusion gene name: FAM118A-VAPB
Fusion gene ID: hg55007tg9217
HgeneTgene
Gene symbol

FAM118A

VAPB

Gene ID

55007

9217

Gene namefamily with sequence similarity 118 member AVAMP associated protein B and C
SynonymsC22orf8ALS8|VAMP-B|VAP-B
Cytomap('FAM118A')('VAPB')

22q13.31

20q13.32

Type of geneprotein-codingprotein-coding
Descriptionprotein FAM118AbK268H5.C22.4vesicle-associated membrane protein-associated protein B/CVAMP (vesicle-associated membrane protein)-associated protein B and CVAMP-associated 33 kDa protein
Modification date2020032720200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000216214, ENST00000405673, 
ENST00000441876, ENST00000405548, 
ENST00000491671, 
Fusion gene scores* DoF score11 X 7 X 8=61611 X 11 X 6=726
# samples 1112
** MAII scorelog2(11/616*10)=-2.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(12/726*10)=-2.59693514238723
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: FAM118A [Title/Abstract] AND VAPB [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointFAM118A(45706064)-VAPB(57009658), # samples:2
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
TgeneVAPB

GO:0019048

modulation by virus of host morphology or physiology

16227268

TgeneVAPB

GO:0036498

IRE1-mediated unfolded protein response

20940299



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-KD-A5QS-01AFAM118Achr22

45706064

+VAPBchr20

57009658

+
ChimerDB4SARCTCGA-KD-A5QS-01AFAM118Achr22

45706064

-VAPBchr20

57014001

+


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Fusion Gene ORF analysis for FAM118A-VAPB

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
5UTR-3CDSENST00000216214ENST00000475243FAM118Achr22

45706064

+VAPBchr20

57009658

+
5UTR-3CDSENST00000216214ENST00000475243FAM118Achr22

45706064

-VAPBchr20

57014001

+
5UTR-3CDSENST00000405673ENST00000475243FAM118Achr22

45706064

+VAPBchr20

57009658

+
5UTR-3CDSENST00000405673ENST00000475243FAM118Achr22

45706064

-VAPBchr20

57014001

+
5UTR-3CDSENST00000441876ENST00000475243FAM118Achr22

45706064

+VAPBchr20

57009658

+
5UTR-3CDSENST00000441876ENST00000475243FAM118Achr22

45706064

-VAPBchr20

57014001

+
5UTR-3UTRENST00000216214ENST00000265619FAM118Achr22

45706064

-VAPBchr20

57014001

+
5UTR-3UTRENST00000405673ENST00000265619FAM118Achr22

45706064

-VAPBchr20

57014001

+
5UTR-3UTRENST00000441876ENST00000265619FAM118Achr22

45706064

-VAPBchr20

57014001

+
5UTR-intronENST00000216214ENST00000265619FAM118Achr22

45706064

+VAPBchr20

57009658

+
5UTR-intronENST00000216214ENST00000395802FAM118Achr22

45706064

+VAPBchr20

57009658

+
5UTR-intronENST00000216214ENST00000395802FAM118Achr22

45706064

-VAPBchr20

57014001

+
5UTR-intronENST00000405673ENST00000265619FAM118Achr22

45706064

+VAPBchr20

57009658

+
5UTR-intronENST00000405673ENST00000395802FAM118Achr22

45706064

+VAPBchr20

57009658

+
5UTR-intronENST00000405673ENST00000395802FAM118Achr22

45706064

-VAPBchr20

57014001

+
5UTR-intronENST00000441876ENST00000265619FAM118Achr22

45706064

+VAPBchr20

57009658

+
5UTR-intronENST00000441876ENST00000395802FAM118Achr22

45706064

+VAPBchr20

57009658

+
5UTR-intronENST00000441876ENST00000395802FAM118Achr22

45706064

-VAPBchr20

57014001

+
intron-3CDSENST00000405548ENST00000475243FAM118Achr22

45706064

+VAPBchr20

57009658

+
intron-3CDSENST00000405548ENST00000475243FAM118Achr22

45706064

-VAPBchr20

57014001

+
intron-3CDSENST00000491671ENST00000475243FAM118Achr22

45706064

+VAPBchr20

57009658

+
intron-3CDSENST00000491671ENST00000475243FAM118Achr22

45706064

-VAPBchr20

57014001

+
intron-3UTRENST00000405548ENST00000265619FAM118Achr22

45706064

-VAPBchr20

57014001

+
intron-3UTRENST00000491671ENST00000265619FAM118Achr22

45706064

-VAPBchr20

57014001

+
intron-intronENST00000405548ENST00000265619FAM118Achr22

45706064

+VAPBchr20

57009658

+
intron-intronENST00000405548ENST00000395802FAM118Achr22

45706064

+VAPBchr20

57009658

+
intron-intronENST00000405548ENST00000395802FAM118Achr22

45706064

-VAPBchr20

57014001

+
intron-intronENST00000491671ENST00000265619FAM118Achr22

45706064

+VAPBchr20

57009658

+
intron-intronENST00000491671ENST00000395802FAM118Achr22

45706064

+VAPBchr20

57009658

+
intron-intronENST00000491671ENST00000395802FAM118Achr22

45706064

-VAPBchr20

57014001

+

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 FAM118A-VAPB


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)
FAM118Achr2245706064+VAPBchr2057009657+1.83E-050.99998164
FAM118Achr2245706064+VAPBchr2057009657+1.83E-050.99998164


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 FAM118A-VAPB


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/:45706064/:57009658)
- 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 FAM118A-VAPB


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 FAM118A-VAPB


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 FAM118A-VAPB


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 FAM118A-VAPB


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC1837728AMYOTROPHIC LATERAL SCLEROSIS 8 (disorder)4CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC1854058SPINAL MUSCULAR ATROPHY, LATE-ONSET, FINKEL TYPE2GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC1866777Spinal Muscular Atrophy, Proximal, Adult, Autosomal Dominant2CTD_human;ORPHANET
TgeneC0002736Amyotrophic Lateral Sclerosis1ORPHANET