UTHEALTH HOME    ABOUT SBMI    A-Z    WEBMAIL    INSIDE THE UNIVERSITY
FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact

Terms of Use

Center for Computational Systems Medicine level2
leaf

Fusion Gene Summary

leaf

Fusion Gene Sample Information

leaf

Fusion ORF Analysis

leaf

Fusion Amino Acid Sequences

leaf

Fusion Protein Functional Features

leaf

Fusion Protein Structure

leaf

pLDDT scores

leaf

Ramachandran Plot of Fusion Protein Structure

leaf

Fusion Protein-Protein Interaction

leaf

Related drugs with this fusion protein

leaf

Related disease with this fusion protein

Fusion Protein:VTI1A-HDAC1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: VTI1A-HDAC1
FusionPDB ID: 98590
FusionGDB2.0 ID: 98590
HgeneTgene
Gene symbol

VTI1A

HDAC1

Gene ID

143187

3065

Gene namevesicle transport through interaction with t-SNAREs 1Ahistone deacetylase 1
SynonymsMMDS3|MVti1|VTI1RP2|Vti1-rp2GON-10|HD1|KDAC1|RPD3|RPD3L1
Cytomap

10q25.2

1p35.2-p35.1

Type of geneprotein-codingprotein-coding
Descriptionvesicle transport through interaction with t-SNAREs homolog 1ASNARE Vti1a-beta proteinvesicle transport v-SNARE protein Vti1-like 2histone deacetylase 1reduced potassium dependency, yeast homolog-like 1
Modification date2020031320200327
UniProtAcc

Q96AJ9

Q96DB2

Ensembl transtripts involved in fusion geneENST idsENST00000393077, ENST00000432306, 
ENST00000483122, 
ENST00000373541, 
ENST00000490081, ENST00000373548, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score15 X 12 X 12=216012 X 11 X 6=792
# samples 2413
** MAII scorelog2(24/2160*10)=-3.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(13/792*10)=-2.60698880705116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: VTI1A [Title/Abstract] AND HDAC1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)VTI1A(114298089)-HDAC1(32790080), # samples:3
Anticipated loss of major functional domain due to fusion event.VTI1A-HDAC1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
VTI1A-HDAC1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame 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
HgeneVTI1A

GO:0042147

retrograde transport, endosome to Golgi

15215310|18195106

TgeneHDAC1

GO:0000122

negative regulation of transcription by RNA polymerase II

18854353

TgeneHDAC1

GO:0006476

protein deacetylation

17172643|23629966

TgeneHDAC1

GO:0045893

positive regulation of transcription, DNA-templated

16762839

TgeneHDAC1

GO:0045944

positive regulation of transcription by RNA polymerase II

16762839

TgeneHDAC1

GO:0060766

negative regulation of androgen receptor signaling pathway

15919722

TgeneHDAC1

GO:0070932

histone H3 deacetylation

12590135

TgeneHDAC1

GO:0070933

histone H4 deacetylation

12590135


check buttonFusion gene breakpoints across VTI1A (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 HDAC1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


Top

Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4UCSTCGA-N9-A4Q1-01AVTI1Achr10

114298089

-HDAC1chr1

32790080

+
ChimerDB4UCSTCGA-N9-A4Q1-01AVTI1Achr10

114298089

+HDAC1chr1

32790080

+
ChimerDB4UCSTCGA-N9-A4Q1VTI1Achr10

114298089

+HDAC1chr1

32790079

+
ChimerDB4UCSTCGA-N9-A4Q1VTI1Achr10

114298089

+HDAC1chr1

32790080

+


Top

Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000432306VTI1Achr10114298089+ENST00000373548HDAC1chr132790080+2303543861711541
ENST00000393077VTI1Achr10114298089+ENST00000373548HDAC1chr132790080+2303543861711541
ENST00000432306VTI1Achr10114298089+ENST00000373548HDAC1chr132790079+2303543861711541
ENST00000393077VTI1Achr10114298089+ENST00000373548HDAC1chr132790079+2303543861711541

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
ENST00000432306ENST00000373548VTI1Achr10114298089+HDAC1chr132790080+0.0005571920.99944276
ENST00000393077ENST00000373548VTI1Achr10114298089+HDAC1chr132790080+0.0005571920.99944276
ENST00000432306ENST00000373548VTI1Achr10114298089+HDAC1chr132790079+0.0005571920.99944276
ENST00000393077ENST00000373548VTI1Achr10114298089+HDAC1chr132790079+0.0005571920.99944276

Top

Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>98590_98590_1_VTI1A-HDAC1_VTI1A_chr10_114298089_ENST00000393077_HDAC1_chr1_32790079_ENST00000373548_length(amino acids)=541AA_BP=152
MAWATRSGAAMSSDFEGYEQDFAVLTAEITSKIARVPRLPPDEKKQMVANVEKQLEEAKELLEQMDLEVREIPPQSRGMYSNRMRSYKQE
MGKLETDFKRSRIAYSDEVRNELLGDDGNSSENQRAHLLDNTERLERSSRRLEAGYQIAVETVNVGEDCPVFDGLFEFCQLSTGGSVASA
VKLNKQQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDL
RDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGG
GYTIRNVARCWTYETAVALDTEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTNEYLEKIKQRLFENLRMLPHAPGVQMQAIPEDAIPE
ESGDEDEDDPDKRISICSSDKRIACEEEFSDSEEEGEGGRKNSSNFKKAKRVKTEDEKEKDPEEKKEVTEEEKTKEEKPEAKGVKEEVKL

--------------------------------------------------------------

>98590_98590_2_VTI1A-HDAC1_VTI1A_chr10_114298089_ENST00000393077_HDAC1_chr1_32790080_ENST00000373548_length(amino acids)=541AA_BP=152
MAWATRSGAAMSSDFEGYEQDFAVLTAEITSKIARVPRLPPDEKKQMVANVEKQLEEAKELLEQMDLEVREIPPQSRGMYSNRMRSYKQE
MGKLETDFKRSRIAYSDEVRNELLGDDGNSSENQRAHLLDNTERLERSSRRLEAGYQIAVETVNVGEDCPVFDGLFEFCQLSTGGSVASA
VKLNKQQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDL
RDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGG
GYTIRNVARCWTYETAVALDTEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTNEYLEKIKQRLFENLRMLPHAPGVQMQAIPEDAIPE
ESGDEDEDDPDKRISICSSDKRIACEEEFSDSEEEGEGGRKNSSNFKKAKRVKTEDEKEKDPEEKKEVTEEEKTKEEKPEAKGVKEEVKL

--------------------------------------------------------------

>98590_98590_3_VTI1A-HDAC1_VTI1A_chr10_114298089_ENST00000432306_HDAC1_chr1_32790079_ENST00000373548_length(amino acids)=541AA_BP=152
MAWATRSGAAMSSDFEGYEQDFAVLTAEITSKIARVPRLPPDEKKQMVANVEKQLEEAKELLEQMDLEVREIPPQSRGMYSNRMRSYKQE
MGKLETDFKRSRIAYSDEVRNELLGDDGNSSENQRAHLLDNTERLERSSRRLEAGYQIAVETVNVGEDCPVFDGLFEFCQLSTGGSVASA
VKLNKQQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDL
RDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGG
GYTIRNVARCWTYETAVALDTEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTNEYLEKIKQRLFENLRMLPHAPGVQMQAIPEDAIPE
ESGDEDEDDPDKRISICSSDKRIACEEEFSDSEEEGEGGRKNSSNFKKAKRVKTEDEKEKDPEEKKEVTEEEKTKEEKPEAKGVKEEVKL

--------------------------------------------------------------

>98590_98590_4_VTI1A-HDAC1_VTI1A_chr10_114298089_ENST00000432306_HDAC1_chr1_32790080_ENST00000373548_length(amino acids)=541AA_BP=152
MAWATRSGAAMSSDFEGYEQDFAVLTAEITSKIARVPRLPPDEKKQMVANVEKQLEEAKELLEQMDLEVREIPPQSRGMYSNRMRSYKQE
MGKLETDFKRSRIAYSDEVRNELLGDDGNSSENQRAHLLDNTERLERSSRRLEAGYQIAVETVNVGEDCPVFDGLFEFCQLSTGGSVASA
VKLNKQQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDL
RDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGG
GYTIRNVARCWTYETAVALDTEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTNEYLEKIKQRLFENLRMLPHAPGVQMQAIPEDAIPE
ESGDEDEDDPDKRISICSSDKRIACEEEFSDSEEEGEGGRKNSSNFKKAKRVKTEDEKEKDPEEKKEVTEEEKTKEEKPEAKGVKEEVKL

--------------------------------------------------------------

Top

Fusion Protein Functional Features


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/chr10:114298089/chr1:32790080)
- 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
VTI1A

Q96AJ9

HDAC1

Q96DB2

FUNCTION: V-SNARE that mediates vesicle transport pathways through interactions with t-SNAREs on the target membrane. These interactions are proposed to mediate aspects of the specificity of vesicle trafficking and to promote fusion of the lipid bilayers. Involved in vesicular transport from the late endosomes to the trans-Golgi network. Along with VAMP7, involved in an non-conventional RAB1-dependent traffic route to the cell surface used by KCNIP1 and KCND2. May be involved in increased cytokine secretion associated with cellular senescence. {ECO:0000269|PubMed:18195106, ECO:0000269|PubMed:19138172}.FUNCTION: Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. {ECO:0000269|PubMed:11948178}.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneVTI1Achr10:114298089chr1:32790079ENST00000393077+5831_92142.33333333333334218.0Coiled coilOntology_term=ECO:0000255
HgeneVTI1Achr10:114298089chr1:32790079ENST00000432306+5831_92142.33333333333334204.0Coiled coilOntology_term=ECO:0000255
HgeneVTI1Achr10:114298089chr1:32790080ENST00000393077+5831_92142.33333333333334218.0Coiled coilOntology_term=ECO:0000255
HgeneVTI1Achr10:114298089chr1:32790080ENST00000432306+5831_92142.33333333333334204.0Coiled coilOntology_term=ECO:0000255

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneVTI1Achr10:114298089chr1:32790079ENST00000393077+58112_178142.33333333333334218.0Coiled coilOntology_term=ECO:0000255
HgeneVTI1Achr10:114298089chr1:32790079ENST00000432306+58112_178142.33333333333334204.0Coiled coilOntology_term=ECO:0000255
HgeneVTI1Achr10:114298089chr1:32790080ENST00000393077+58112_178142.33333333333334218.0Coiled coilOntology_term=ECO:0000255
HgeneVTI1Achr10:114298089chr1:32790080ENST00000432306+58112_178142.33333333333334204.0Coiled coilOntology_term=ECO:0000255
HgeneVTI1Achr10:114298089chr1:32790079ENST00000393077+581_192142.33333333333334218.0Topological domainCytoplasmic
HgeneVTI1Achr10:114298089chr1:32790079ENST00000393077+58214_217142.33333333333334218.0Topological domainExtracellular
HgeneVTI1Achr10:114298089chr1:32790079ENST00000432306+581_192142.33333333333334204.0Topological domainCytoplasmic
HgeneVTI1Achr10:114298089chr1:32790079ENST00000432306+58214_217142.33333333333334204.0Topological domainExtracellular
HgeneVTI1Achr10:114298089chr1:32790080ENST00000393077+581_192142.33333333333334218.0Topological domainCytoplasmic
HgeneVTI1Achr10:114298089chr1:32790080ENST00000393077+58214_217142.33333333333334218.0Topological domainExtracellular
HgeneVTI1Achr10:114298089chr1:32790080ENST00000432306+581_192142.33333333333334204.0Topological domainCytoplasmic
HgeneVTI1Achr10:114298089chr1:32790080ENST00000432306+58214_217142.33333333333334204.0Topological domainExtracellular
HgeneVTI1Achr10:114298089chr1:32790079ENST00000393077+58193_213142.33333333333334218.0TransmembraneHelical
HgeneVTI1Achr10:114298089chr1:32790079ENST00000432306+58193_213142.33333333333334204.0TransmembraneHelical
HgeneVTI1Achr10:114298089chr1:32790080ENST00000393077+58193_213142.33333333333334218.0TransmembraneHelical
HgeneVTI1Achr10:114298089chr1:32790080ENST00000432306+58193_213142.33333333333334204.0TransmembraneHelical
TgeneHDAC1chr10:114298089chr1:32790079ENST000003735482149_32193.33333333333333483.0RegionNote=Histone deacetylase
TgeneHDAC1chr10:114298089chr1:32790080ENST000003735482149_32193.33333333333333483.0RegionNote=Histone deacetylase


Top

Fusion Protein Structures

check button PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
Fusion protein PDB link (fusion AA seq ID in FusionPDB)HgeneHchrHbpHstrandTgeneTchrTbpTstrandAA seqLen(AA seq)
PDB file >>>1157_VTI1A_114298089_HDAC1_32790080_1157_VTI1A_114298089_HDAC1_32790080_ranked_0.pdbVTI1A114298089114298089ENST00000373548HDAC1chr132790080+
MAWATRSGAAMSSDFEGYEQDFAVLTAEITSKIARVPRLPPDEKKQMVANVEKQLEEAKELLEQMDLEVREIPPQSRGMYSNRMRSYKQE
MGKLETDFKRSRIAYSDEVRNELLGDDGNSSENQRAHLLDNTERLERSSRRLEAGYQIAVETVNVGEDCPVFDGLFEFCQLSTGGSVASA
VKLNKQQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDL
RDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGG
GYTIRNVARCWTYETAVALDTEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTNEYLEKIKQRLFENLRMLPHAPGVQMQAIPEDAIPE
ESGDEDEDDPDKRISICSSDKRIACEEEFSDSEEEGEGGRKNSSNFKKAKRVKTEDEKEKDPEEKKEVTEEEKTKEEKPEAKGVKEEVKL
541


Top

pLDDT score distribution

check button pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
VTI1A_pLDDT.png
all structure
all structure
HDAC1_pLDDT.png
all structure
all structure

check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
all structure


Top

Ramachandran Plot of Fusion Protein Structure


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.
Fusion AA seq ID in FusionPDB and their Ramachandran plots

Top

Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors
VTI1AVAMP4, VAMP3, STX7, STX8, VAMP8, env, TMBIM6, STX6, STX12, CLEC12A, Snap29, HAUS1, HNRNPL, RNF4, BET1, APEX1, NAPA, VAMP5, ORF7b, ARF6, B3GAT1, LAMP2, LAMP3, LAMTOR1, MARCKS, RAB2A, RAB4A, RAB5A, RAB5C, RAB9A, EDEM1, TRPC4AP, TMEM74, ZDHHC12, SEC22B, SMPD1, TMEM9, NAPG, TMEM9B, GPRC5B, B4GALT5, TMEM171, ASPH, SLC39A4, VPS45, SNAP29, HLA-C, STX11, STX18,


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
VTI1Aall structure
HDAC1


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


Top

Related Drugs to VTI1A-HDAC1


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

Top

Related Diseases to VTI1A-HDAC1


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneVTI1AC0001418Adenocarcinoma1CTD_human
HgeneVTI1AC0009402Colorectal Carcinoma1CTD_human
HgeneVTI1AC0009404Colorectal Neoplasms1CTD_human
HgeneVTI1AC0205641Adenocarcinoma, Basal Cell1CTD_human
HgeneVTI1AC0205642Adenocarcinoma, Oxyphilic1CTD_human
HgeneVTI1AC0205643Carcinoma, Cribriform1CTD_human
HgeneVTI1AC0205644Carcinoma, Granular Cell1CTD_human
HgeneVTI1AC0205645Adenocarcinoma, Tubular1CTD_human