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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 41492

FusionGeneSummary for VMP1_KRTAP4-6

check button Fusion gene summary
Fusion gene informationFusion gene name: VMP1_KRTAP4-6
Fusion gene ID: 41492
HgeneTgene
Gene symbol

VMP1

KRTAP4-6

Gene ID

81671

81871

Gene namevacuole membrane protein 1keratin associated protein 4-6
SynonymsEPG3|TANGO5|TMEM49KAP4.15|KAP4.6|KRTAP4-15|KRTAP4.15
Cytomap

17q23.1

17q21.2

Type of geneprotein-codingprotein-coding
Descriptionvacuole membrane protein 1ectopic P-granules autophagy protein 3 homologtransmembrane protein 49transport and golgi organization 5 homologkeratin-associated protein 4-6keratin associated protein 4-15keratin-associated protein 4.6ultrahigh sulfur keratin-associated protein 4.15
Modification date2018052320180329
UniProtAcc

Q96GC9

Q9BYQ5

Ensembl transtripts involved in fusion geneENST00000262291, ENST00000537567, 
ENST00000539763, ENST00000536180, 
ENST00000545362, ENST00000588617, 
ENST00000345847, 
Fusion gene scores* DoF score19 X 10 X 9=17101 X 1 X 1=1
# samples 181
** MAII scorelog2(18/1710*10)=-3.24792751344359
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(1/1*10)=3.32192809488736
Context

PubMed: VMP1 [Title/Abstract] AND KRTAP4-6 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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 three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGALDCOADTCGA-AZ-4323-01AVMP1chr17

57816308

+KRTAP4-6chr17

39296700

-
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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
In-frameENST00000262291ENST00000345847VMP1chr17

57816308

+KRTAP4-6chr17

39296700

-
intron-3CDSENST00000537567ENST00000345847VMP1chr17

57816308

+KRTAP4-6chr17

39296700

-
5UTR-3CDSENST00000539763ENST00000345847VMP1chr17

57816308

+KRTAP4-6chr17

39296700

-
In-frameENST00000536180ENST00000345847VMP1chr17

57816308

+KRTAP4-6chr17

39296700

-
In-frameENST00000545362ENST00000345847VMP1chr17

57816308

+KRTAP4-6chr17

39296700

-
intron-3CDSENST00000588617ENST00000345847VMP1chr17

57816308

+KRTAP4-6chr17

39296700

-

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FusionProtFeatures for VMP1_KRTAP4-6


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
VMP1

Q96GC9

KRTAP4-6

Q9BYQ5

Stress-induced protein that, when overexpressed,promotes formation of intracellular vacuoles followed by celldeath. May be involved in the cytoplasmic vacuolization of acinarcells during the early stage of acute pancreatitis. Plays a rolein the initial stages of the autophagic process through itsinteraction with BECN1 (By similarity). Involved in cell-celladhesion. Plays an essential role in formation of cell junctions.{ECO:0000250, ECO:0000269|PubMed:17724469}. In the hair cortex, hair keratin intermediate filamentsare embedded in an interfilamentous matrix, consisting of hairkeratin-associated proteins (KRTAP), which are essential for theformation of a rigid and resistant hair shaft through theirextensive disulfide bond cross-linking with abundant cysteineresidues of hair keratins. The matrix proteins include the high-sulfur and high-glycine-tyrosine keratins.

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
HgeneVMP1chr17:57816308chr17:39296700ENST00000262291+5122_43138407Topological domainCytoplasmic
HgeneVMP1chr17:57816308chr17:39296700ENST00000262291+51265_77138407Topological domainExtracellular
HgeneVMP1chr17:57816308chr17:39296700ENST00000262291+51299_109138407Topological domainCytoplasmic
HgeneVMP1chr17:57816308chr17:39296700ENST00000262291+512110_130138407TransmembraneHelical
HgeneVMP1chr17:57816308chr17:39296700ENST00000262291+51244_64138407TransmembraneHelical
HgeneVMP1chr17:57816308chr17:39296700ENST00000262291+51278_98138407TransmembraneHelical
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-0120_1730206RegionNote=30 X 5 AA repeats of C-C-[IRQVEL]-[SPTR]-[STVQRCP]
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-01104_1080206RepeatNote=18
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-01114_1180206RepeatNote=19
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-01119_1230206RepeatNote=20
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-01124_1280206RepeatNote=21
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-01129_1330206RepeatNote=22
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-01134_1380206RepeatNote=23
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-01139_1430206RepeatNote=24
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-01144_1480206RepeatNote=25
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-01149_1530206RepeatNote=26
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-01154_1580206RepeatNote=27
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-01159_1630206RepeatNote=28
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-01164_1680206RepeatNote=29
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-01169_1730206RepeatNote=30
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-0120_240206RepeatNote=1
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-0125_290206RepeatNote=2
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-0130_340206RepeatNote=3
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-0135_390206RepeatNote=4
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-0140_440206RepeatNote=5
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-0145_490206RepeatNote=6
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-0150_540206RepeatNote=7
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-0155_590206RepeatNote=8
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-0160_640206RepeatNote=9
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-0165_680206RepeatNote=10
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-0169_730206RepeatNote=11
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-0174_780206RepeatNote=12
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-0179_830206RepeatNote=13
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-0184_880206RepeatNote=14
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-0189_930206RepeatNote=15
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-0194_980206RepeatNote=16
TgeneKRTAP4-6chr17:57816308chr17:39296700ENST00000345847-0199_1030206RepeatNote=17

- In-frame and not-retained protein feature among the 13 regional features.
>>>>>>>>>
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneVMP1chr17:57816308chr17:39296700ENST00000262291+512131_250138407Topological domainExtracellular
HgeneVMP1chr17:57816308chr17:39296700ENST00000262291+512272_273138407Topological domainCytoplasmic
HgeneVMP1chr17:57816308chr17:39296700ENST00000262291+512295_305138407Topological domainExtracellular
HgeneVMP1chr17:57816308chr17:39296700ENST00000262291+512327_363138407Topological domainCytoplasmic
HgeneVMP1chr17:57816308chr17:39296700ENST00000262291+512385_406138407Topological domainExtracellular
HgeneVMP1chr17:57816308chr17:39296700ENST00000262291+512251_271138407TransmembraneHelical
HgeneVMP1chr17:57816308chr17:39296700ENST00000262291+512274_294138407TransmembraneHelical
HgeneVMP1chr17:57816308chr17:39296700ENST00000262291+512306_326138407TransmembraneHelical
HgeneVMP1chr17:57816308chr17:39296700ENST00000262291+512364_384138407TransmembraneHelical


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FusionGeneSequence for VMP1_KRTAP4-6


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.
>In-frame_VMP1_ENST00000262291_chr17_57816308_+_KRTAP4-6_ENST00000345847_chr17_39296700_-_138aa
MAENGKNCDQRRVAMNKEHHNGNFTDPSSVNEKKRREREERQNIVLWRQPLITLQTFSLEILVILKEWTSKLWHRQSIVVSFLLLLAVLI

>In-frame_VMP1_ENST00000536180_chr17_57816308_+_KRTAP4-6_ENST00000345847_chr17_39296700_-_41aa

>In-frame_VMP1_ENST00000545362_chr17_57816308_+_KRTAP4-6_ENST00000345847_chr17_39296700_-_138aa
MAENGKNCDQRRVAMNKEHHNGNFTDPSSVNEKKRREREERQNIVLWRQPLITLQTFSLEILVILKEWTSKLWHRQSIVVSFLLLLAVLI


* Fusion transcript sequences (only coding sequence (CDS) region).
>In-frame_VMP1_ENST00000262291_chr17_57816308_+_KRTAP4-6_ENST00000345847_chr17_39296700_-_414nt
ATGGCAGAGAATGGAAAAAATTGTGACCAGAGACGTGTAGCAATGAACAAGGAACATCATAATGGAAATTTCACAGACCCCTCTTCAGTG
AATGAAAAGAAGAGGAGGGAGCGGGAAGAAAGGCAGAATATTGTCCTGTGGAGACAGCCGCTCATTACCTTGCAGTATTTTTCTCTGGAA
ATCCTTGTAATCTTGAAGGAATGGACCTCAAAATTATGGCATCGTCAAAGCATTGTGGTGTCTTTTTTACTGCTGCTTGCTGTGCTTATA
GCTACGTATTATGTTGAAGGAGTGCATCAACAGTATGTGCAACGTATAGAGAAACAGTTTCTTTTGTATGCCTACTGGATAGGCTTAGGA

>In-frame_VMP1_ENST00000536180_chr17_57816308_+_KRTAP4-6_ENST00000345847_chr17_39296700_-_123nt
ATGGACCTCAAATATGTGCAACGTATAGAGAAACAGTTTCTTTTGTATGCCTACTGGATAGGCTTAGGAATTTTGTCTTCTGTTGGGCTT

>In-frame_VMP1_ENST00000545362_chr17_57816308_+_KRTAP4-6_ENST00000345847_chr17_39296700_-_414nt
ATGGCAGAGAATGGAAAAAATTGTGACCAGAGACGTGTAGCAATGAACAAGGAACATCATAATGGAAATTTCACAGACCCCTCTTCAGTG
AATGAAAAGAAGAGGAGGGAGCGGGAAGAAAGGCAGAATATTGTCCTGTGGAGACAGCCGCTCATTACCTTGCAGTATTTTTCTCTGGAA
ATCCTTGTAATCTTGAAGGAATGGACCTCAAAATTATGGCATCGTCAAAGCATTGTGGTGTCTTTTTTACTGCTGCTTGCTGTGCTTATA
GCTACGTATTATGTTGAAGGAGTGCATCAACAGTATGTGCAACGTATAGAGAAACAGTTTCTTTTGTATGCCTACTGGATAGGCTTAGGA


* Fusion transcript sequences (Full-length transcript).
>In-frame_VMP1_ENST00000262291_chr17_57816308_+_KRTAP4-6_ENST00000345847_chr17_39296700_-_763nt
GACAAGTTCCGGATCAAGAATCACAAAGCGAGCAGTCATTCTTCCTCTTGCCACACCCACAGGGCCCGCACTAAGAGCCTAACTGAAATC
CCGCGAGGATCAACCGAGCTCGCCGAAAGGAGGGAGGAACGTATCCCTTCTGGAGGCTGTCTCAGGGGGCAGAGGGACCGGACCGGAAGT
GACGTGAGCGGGTTCCGGTTGTCTGGAGCCCAGCGGCGGGTGTGAGAGTCCGTAAGGAGCAGCTTCCAGGATCCTGAGATCCGGAGCAGC
CGGGGTCGGAGCGGCTCCTCAAGAGTTACTGATCTATGAAATGGCAGAGAATGGAAAAAATTGTGACCAGAGACGTGTAGCAATGAACAA
GGAACATCATAATGGAAATTTCACAGACCCCTCTTCAGTGAATGAAAAGAAGAGGAGGGAGCGGGAAGAAAGGCAGAATATTGTCCTGTG
GAGACAGCCGCTCATTACCTTGCAGTATTTTTCTCTGGAAATCCTTGTAATCTTGAAGGAATGGACCTCAAAATTATGGCATCGTCAAAG
CATTGTGGTGTCTTTTTTACTGCTGCTTGCTGTGCTTATAGCTACGTATTATGTTGAAGGAGTGCATCAACAGTATGTGCAACGTATAGA
GAAACAGTTTCTTTTGTATGCCTACTGGATAGGCTTAGGAATTTTGTCTTCTGTTGGGCTTGGAACAGGGCTGCACACCTTTCTGCTTTA

>In-frame_VMP1_ENST00000536180_chr17_57816308_+_KRTAP4-6_ENST00000345847_chr17_39296700_-_472nt
GTCTGGAGCCCAGCGGCGGGTGTGAGAGTCCGTAAGGAGCAGCTTCCAGGATCCTGAGATCCGGAGCAGCCGGGGTCGGAGCGGCTCCTC
AAGAGTTACTGATCTATGAAATGGCAGAGAATGGAAAAAATTGTGACCAGAGACGTGTAGCAATGAACAAGGAACATCATAATGGAAATT
TCACAGACCCCTCTTCAGTGAATGAAAAGAAGAGGAGGGAGCGGGAAGAAAGGCAGAATATTGTCCTGTGGAGACAGCCGCTCATTACCT
TGCAGTATTTTTCTCTGGAAATCCTTGTAATCTTGAAGGAATGGACCTCAAATATGTGCAACGTATAGAGAAACAGTTTCTTTTGTATGC
CTACTGGATAGGCTTAGGAATTTTGTCTTCTGTTGGGCTTGGAACAGGGCTGCACACCTTTCTGCTTTATCTGATGGTCAGCTCCTGTTG

>In-frame_VMP1_ENST00000545362_chr17_57816308_+_KRTAP4-6_ENST00000345847_chr17_39296700_-_506nt
GATCCGGAGCAGCCGGGGTCGGAGCGGCTCCTCAAGAGTTACTGATCTATGAAATGGCAGAGAATGGAAAAAATTGTGACCAGAGACGTG
TAGCAATGAACAAGGAACATCATAATGGAAATTTCACAGACCCCTCTTCAGTGAATGAAAAGAAGAGGAGGGAGCGGGAAGAAAGGCAGA
ATATTGTCCTGTGGAGACAGCCGCTCATTACCTTGCAGTATTTTTCTCTGGAAATCCTTGTAATCTTGAAGGAATGGACCTCAAAATTAT
GGCATCGTCAAAGCATTGTGGTGTCTTTTTTACTGCTGCTTGCTGTGCTTATAGCTACGTATTATGTTGAAGGAGTGCATCAACAGTATG
TGCAACGTATAGAGAAACAGTTTCTTTTGTATGCCTACTGGATAGGCTTAGGAATTTTGTCTTCTGTTGGGCTTGGAACAGGGCTGCACA


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FusionGenePPI for VMP1_KRTAP4-6


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
VMP1HGS, ELAVL1, TJP1, KLK11, LPAR6, ERGIC3, FAF2, KRAS, TCTN2, TCTN3, TMEM216, DPEP1, CDH13, MAS1, LMNAKRTAP4-6


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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RelatedDrugs for VMP1_KRTAP4-6


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for VMP1_KRTAP4-6


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