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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: 16402

FusionGeneSummary for HLTF_TM4SF1

check button Fusion gene summary
Fusion gene informationFusion gene name: HLTF_TM4SF1
Fusion gene ID: 16402
HgeneTgene
Gene symbol

HLTF

TM4SF1

Gene ID

6596

4071

Gene namehelicase like transcription factortransmembrane 4 L six family member 1
SynonymsHIP116|HIP116A|HLTF1|RNF80|SMARCA3|SNF2L3|ZBU1H-L6|L6|M3S1|TAAL6
Cytomap

3q24

3q25.1

Type of geneprotein-codingprotein-coding
Descriptionhelicase-like transcription factorDNA-binding protein/plasminogen activator inhibitor-1 regulatorRING finger protein 80RING-type E3 ubiquitin transferase HLTFSNF2-like 3SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfatransmembrane 4 L6 family member 1membrane component, chromosome 3, surface marker 1transmembrane 4 superfamily member 1tumor-associated antigen L6
Modification date2018051920180523
UniProtAcc

Q14527

P30408

Ensembl transtripts involved in fusion geneENST00000465259, ENST00000310053, 
ENST00000392912, ENST00000494055, 
ENST00000481663, 
ENST00000305366, 
ENST00000472441, 
Fusion gene scores* DoF score2 X 2 X 2=87 X 5 X 4=140
# samples 27
** MAII scorelog2(2/8*10)=1.32192809488736log2(7/140*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HLTF [Title/Abstract] AND TM4SF1 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotationTumor suppressor gene involved fusion gene, retained protein feature but frameshift.
DDR (DNA damage repair) gene involved fusion gene, in-frame but not retained their domain.
DDR (DNA damage repair) gene involved fusion gene, retained protein feature but frameshift.
* 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
TCGALDSTADTCGA-BR-8060-01AHLTFchr3

148759953

-TM4SF1chr3

149093556

-
* 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
Frame-shitENST00000465259ENST00000305366HLTFchr3

148759953

-TM4SF1chr3

149093556

-
5CDS-intronENST00000465259ENST00000472441HLTFchr3

148759953

-TM4SF1chr3

149093556

-
Frame-shitENST00000310053ENST00000305366HLTFchr3

148759953

-TM4SF1chr3

149093556

-
5CDS-intronENST00000310053ENST00000472441HLTFchr3

148759953

-TM4SF1chr3

149093556

-
Frame-shitENST00000392912ENST00000305366HLTFchr3

148759953

-TM4SF1chr3

149093556

-
5CDS-intronENST00000392912ENST00000472441HLTFchr3

148759953

-TM4SF1chr3

149093556

-
Frame-shitENST00000494055ENST00000305366HLTFchr3

148759953

-TM4SF1chr3

149093556

-
5CDS-intronENST00000494055ENST00000472441HLTFchr3

148759953

-TM4SF1chr3

149093556

-
intron-3CDSENST00000481663ENST00000305366HLTFchr3

148759953

-TM4SF1chr3

149093556

-
intron-intronENST00000481663ENST00000472441HLTFchr3

148759953

-TM4SF1chr3

149093556

-

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FusionProtFeatures for HLTF_TM4SF1


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

Q14527

TM4SF1

P30408

Has both helicase and E3 ubiquitin ligase activities.Possesses intrinsic ATP-dependent nucleosome-remodeling activity;This activity may be required for transcriptional activation orrepression of specific target promoters (By similarity). These mayinclude the SERPINE1 and HIV-1 promoters and the SV40 enhancer, towhich this protein can bind directly. Plays a role in error-freepostreplication repair (PRR) of damaged DNA and maintains genomicstability through acting as a ubiquitin ligase for 'Lys-63'-linkedpolyubiquitination of chromatin-bound PCNA. {ECO:0000250,ECO:0000269|PubMed:10391891, ECO:0000269|PubMed:18316726,ECO:0000269|PubMed:18719106, ECO:0000269|PubMed:7876228,ECO:0000269|PubMed:8672239, ECO:0000269|PubMed:9126292}.

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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FusionGeneSequence for HLTF_TM4SF1


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.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for HLTF_TM4SF1


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
HLTFPCNA, UBE2N, UBE2V2, RAD18, USP7, RPAP1, UBE2Z, EWSR1, CHFR, SHPRH, RNF146, ELAVL1, SPRTN, SP1, SP3, NOTCH1, DTL, BRCA1, CDK9, HSPA8, SULT1C2, WBP4, RPA3, RPA2, RPA1, UBC, UBE2A, HLTF, DLD, RNF166, APLF, HIST1H2BA, S100A10, FBXW11, NTRK1, PDK3, SMC1A, EMC2, AP4S1, SYNPO, CERK, TCEAL4, SNW1, CDC5L, NANOG, POU5F1, NFATC1, NFATC2, PMPCA, CHD1L, FEN1, VPRBPTM4SF1DNAJA1, HSPA8, DDR1, ELAVL1, TRIM25


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 HLTF_TM4SF1


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 HLTF_TM4SF1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneHLTFC0022665Kidney Neoplasm1CTD_human