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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:ITGA6-PDK1 (FusionGDB2 ID:HG3655TG5163)

Fusion Gene Summary for ITGA6-PDK1

check button Fusion gene summary
Fusion gene informationFusion gene name: ITGA6-PDK1
Fusion gene ID: hg3655tg5163
HgeneTgene
Gene symbol

ITGA6

PDK1

Gene ID

3655

5163

Gene nameintegrin subunit alpha 6pyruvate dehydrogenase kinase 1
SynonymsCD49f|ITGA6B|VLA-6-
Cytomap('ITGA6')('PDK1')

2q31.1

2q31.1

Type of geneprotein-codingprotein-coding
Descriptionintegrin alpha-6CD49 antigen-like family member Fintegrin alpha6Bintegrin, alpha 6[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 1, mitochondrialpyruvate dehydrogenase (acetyl-transferring) kinase isozyme 1, mitochondrialPDH kinase 1mitochondrial pyruvate dehydrogenase, lipoamide, kinase isoenzyme 1pyruvate dehydroge
Modification date2020032920200329
UniProtAcc

P23229

.
Ensembl transtripts involved in fusion geneENST00000264107, ENST00000343713, 
ENST00000375221, ENST00000409532, 
ENST00000264106, ENST00000409080, 
Fusion gene scores* DoF score10 X 8 X 6=4804 X 5 X 3=60
# samples 125
** MAII scorelog2(12/480*10)=-2
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/60*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ITGA6 [Title/Abstract] AND PDK1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointITGA6(173368979)-PDK1(173420728), # 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


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
ChimerDB4KIRCTCGA-B0-4816-01AITGA6chr2

173368979

+PDK1chr2

173420728

+


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Fusion Gene ORF analysis for ITGA6-PDK1

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-5UTRENST00000264107ENST00000282077ITGA6chr2

173368979

+PDK1chr2

173420728

+
3UTR-5UTRENST00000264107ENST00000392571ITGA6chr2

173368979

+PDK1chr2

173420728

+
3UTR-5UTRENST00000343713ENST00000282077ITGA6chr2

173368979

+PDK1chr2

173420728

+
3UTR-5UTRENST00000343713ENST00000392571ITGA6chr2

173368979

+PDK1chr2

173420728

+
3UTR-5UTRENST00000375221ENST00000282077ITGA6chr2

173368979

+PDK1chr2

173420728

+
3UTR-5UTRENST00000375221ENST00000392571ITGA6chr2

173368979

+PDK1chr2

173420728

+
3UTR-5UTRENST00000409532ENST00000282077ITGA6chr2

173368979

+PDK1chr2

173420728

+
3UTR-5UTRENST00000409532ENST00000392571ITGA6chr2

173368979

+PDK1chr2

173420728

+
3UTR-intronENST00000264107ENST00000410055ITGA6chr2

173368979

+PDK1chr2

173420728

+
3UTR-intronENST00000264107ENST00000543905ITGA6chr2

173368979

+PDK1chr2

173420728

+
3UTR-intronENST00000264107ENST00000544863ITGA6chr2

173368979

+PDK1chr2

173420728

+
3UTR-intronENST00000343713ENST00000410055ITGA6chr2

173368979

+PDK1chr2

173420728

+
3UTR-intronENST00000343713ENST00000543905ITGA6chr2

173368979

+PDK1chr2

173420728

+
3UTR-intronENST00000343713ENST00000544863ITGA6chr2

173368979

+PDK1chr2

173420728

+
3UTR-intronENST00000375221ENST00000410055ITGA6chr2

173368979

+PDK1chr2

173420728

+
3UTR-intronENST00000375221ENST00000543905ITGA6chr2

173368979

+PDK1chr2

173420728

+
3UTR-intronENST00000375221ENST00000544863ITGA6chr2

173368979

+PDK1chr2

173420728

+
3UTR-intronENST00000409532ENST00000410055ITGA6chr2

173368979

+PDK1chr2

173420728

+
3UTR-intronENST00000409532ENST00000543905ITGA6chr2

173368979

+PDK1chr2

173420728

+
3UTR-intronENST00000409532ENST00000544863ITGA6chr2

173368979

+PDK1chr2

173420728

+
5CDS-5UTRENST00000264106ENST00000282077ITGA6chr2

173368979

+PDK1chr2

173420728

+
5CDS-5UTRENST00000264106ENST00000392571ITGA6chr2

173368979

+PDK1chr2

173420728

+
5CDS-5UTRENST00000409080ENST00000282077ITGA6chr2

173368979

+PDK1chr2

173420728

+
5CDS-5UTRENST00000409080ENST00000392571ITGA6chr2

173368979

+PDK1chr2

173420728

+
5CDS-intronENST00000264106ENST00000410055ITGA6chr2

173368979

+PDK1chr2

173420728

+
5CDS-intronENST00000264106ENST00000543905ITGA6chr2

173368979

+PDK1chr2

173420728

+
5CDS-intronENST00000264106ENST00000544863ITGA6chr2

173368979

+PDK1chr2

173420728

+
5CDS-intronENST00000409080ENST00000410055ITGA6chr2

173368979

+PDK1chr2

173420728

+
5CDS-intronENST00000409080ENST00000543905ITGA6chr2

173368979

+PDK1chr2

173420728

+
5CDS-intronENST00000409080ENST00000544863ITGA6chr2

173368979

+PDK1chr2

173420728

+

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 ITGA6-PDK1


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 ITGA6-PDK1


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/:173368979/:173420728)
- 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
ITGA6

P23229

.
FUNCTION: Integrin alpha-6/beta-1 (ITGA6:ITGB1) is a receptor for laminin on platelets (By similarity). Integrin alpha-6/beta-1 (ITGA6:ITGB1) is present in oocytes and is involved in sperm-egg fusion (By similarity). Integrin alpha-6/beta-4 (ITGA6:ITGB4) is a receptor for laminin in epithelial cells and it plays a critical structural role in the hemidesmosome (By similarity). ITGA6:ITGB4 binds to NRG1 (via EGF domain) and this binding is essential for NRG1-ERBB signaling (PubMed:20682778). ITGA6:ITGB4 binds to IGF1 and this binding is essential for IGF1 signaling (PubMed:22351760). ITGA6:ITGB4 binds to IGF2 and this binding is essential for IGF2 signaling (PubMed:28873464). {ECO:0000250|UniProtKB:Q61739, ECO:0000269|PubMed:20682778, ECO:0000269|PubMed:22351760, ECO:0000269|PubMed:28873464}.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 ITGA6-PDK1


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 ITGA6-PDK1


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 ITGA6-PDK1


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 ITGA6-PDK1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneITGA6C1856934Epidermolysis bullosa with pyloric atresia2CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneITGA6C0003873Rheumatoid Arthritis1CTD_human