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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:HCFC1-HCFC1 (FusionGDB2 ID:35730)

Fusion Gene Summary for HCFC1-HCFC1

check button Fusion gene summary
Fusion gene informationFusion gene name: HCFC1-HCFC1
Fusion gene ID: 35730
HgeneTgene
Gene symbol

HCFC1

HCFC1

Gene ID

3054

3054

Gene namehost cell factor C1host cell factor C1
SynonymsCFF|HCF|HCF-1|HCF1|HFC1|MRX3|PPP1R89|VCAFCFF|HCF|HCF-1|HCF1|HFC1|MRX3|PPP1R89|VCAF
Cytomap

Xq28

Xq28

Type of geneprotein-codingprotein-coding
Descriptionhost cell factor 1VP16-accessory proteinprotein phosphatase 1, regulatory subunit 89host cell factor 1VP16-accessory proteinprotein phosphatase 1, regulatory subunit 89
Modification date2020031320200313
UniProtAcc

P51610

Q9NWW0

Ensembl transtripts involved in fusion geneENST00000310441, ENST00000354233, 
ENST00000369984, ENST00000461098, 
ENST00000310441, ENST00000354233, 
ENST00000369984, ENST00000461098, 
Fusion gene scores* DoF score16 X 17 X 8=21766 X 7 X 3=126
# samples 257
** MAII scorelog2(25/2176*10)=-3.12167855658825
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/126*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HCFC1 [Title/Abstract] AND HCFC1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointHCFC1(153220827)-HCFC1(153221692), # samples:1
HCFC1(153214500)-HCFC1(153214565), # 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
HgeneHCFC1

GO:0006355

regulation of transcription, DNA-templated

12670868

HgeneHCFC1

GO:0010628

positive regulation of gene expression

21285374

HgeneHCFC1

GO:0043254

regulation of protein complex assembly

10675337

HgeneHCFC1

GO:0043981

histone H4-K5 acetylation

20018852

HgeneHCFC1

GO:0043982

histone H4-K8 acetylation

20018852

HgeneHCFC1

GO:0043984

histone H4-K16 acetylation

20018852

HgeneHCFC1

GO:0050821

protein stabilization

21285374

TgeneHCFC1

GO:0006355

regulation of transcription, DNA-templated

12670868

TgeneHCFC1

GO:0010628

positive regulation of gene expression

21285374

TgeneHCFC1

GO:0043254

regulation of protein complex assembly

10675337

TgeneHCFC1

GO:0043981

histone H4-K5 acetylation

20018852

TgeneHCFC1

GO:0043982

histone H4-K8 acetylation

20018852

TgeneHCFC1

GO:0043984

histone H4-K16 acetylation

20018852

TgeneHCFC1

GO:0050821

protein stabilization

21285374


check buttonFusion gene breakpoints across HCFC1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across HCFC1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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
ChiTaRS5.0N/AAW836706HCFC1chrX

153220827

+HCFC1chrX

153221692

-
ChiTaRS5.0N/ABQ232509HCFC1chrX

153214500

-HCFC1chrX

153214565

+


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Fusion Gene ORF analysis for HCFC1-HCFC1

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
intron-3CDSENST00000310441ENST00000310441HCFC1chrX

153220827

+HCFC1chrX

153221692

-
intron-3CDSENST00000310441ENST00000354233HCFC1chrX

153220827

+HCFC1chrX

153221692

-
intron-3CDSENST00000310441ENST00000369984HCFC1chrX

153220827

+HCFC1chrX

153221692

-
intron-3CDSENST00000354233ENST00000310441HCFC1chrX

153220827

+HCFC1chrX

153221692

-
intron-3CDSENST00000354233ENST00000354233HCFC1chrX

153220827

+HCFC1chrX

153221692

-
intron-3CDSENST00000354233ENST00000369984HCFC1chrX

153220827

+HCFC1chrX

153221692

-
intron-3CDSENST00000369984ENST00000310441HCFC1chrX

153220827

+HCFC1chrX

153221692

-
intron-3CDSENST00000369984ENST00000354233HCFC1chrX

153220827

+HCFC1chrX

153221692

-
intron-3CDSENST00000369984ENST00000369984HCFC1chrX

153220827

+HCFC1chrX

153221692

-
intron-3CDSENST00000461098ENST00000310441HCFC1chrX

153220827

+HCFC1chrX

153221692

-
intron-3CDSENST00000461098ENST00000354233HCFC1chrX

153220827

+HCFC1chrX

153221692

-
intron-3CDSENST00000461098ENST00000369984HCFC1chrX

153220827

+HCFC1chrX

153221692

-
intron-3UTRENST00000310441ENST00000310441HCFC1chrX

153214500

-HCFC1chrX

153214565

+
intron-3UTRENST00000310441ENST00000354233HCFC1chrX

153214500

-HCFC1chrX

153214565

+
intron-3UTRENST00000310441ENST00000369984HCFC1chrX

153214500

-HCFC1chrX

153214565

+
intron-3UTRENST00000354233ENST00000310441HCFC1chrX

153214500

-HCFC1chrX

153214565

+
intron-3UTRENST00000354233ENST00000354233HCFC1chrX

153214500

-HCFC1chrX

153214565

+
intron-3UTRENST00000354233ENST00000369984HCFC1chrX

153214500

-HCFC1chrX

153214565

+
intron-3UTRENST00000369984ENST00000310441HCFC1chrX

153214500

-HCFC1chrX

153214565

+
intron-3UTRENST00000369984ENST00000354233HCFC1chrX

153214500

-HCFC1chrX

153214565

+
intron-3UTRENST00000369984ENST00000369984HCFC1chrX

153214500

-HCFC1chrX

153214565

+
intron-3UTRENST00000461098ENST00000310441HCFC1chrX

153214500

-HCFC1chrX

153214565

+
intron-3UTRENST00000461098ENST00000354233HCFC1chrX

153214500

-HCFC1chrX

153214565

+
intron-3UTRENST00000461098ENST00000369984HCFC1chrX

153214500

-HCFC1chrX

153214565

+
intron-intronENST00000310441ENST00000461098HCFC1chrX

153220827

+HCFC1chrX

153221692

-
intron-intronENST00000310441ENST00000461098HCFC1chrX

153214500

-HCFC1chrX

153214565

+
intron-intronENST00000354233ENST00000461098HCFC1chrX

153220827

+HCFC1chrX

153221692

-
intron-intronENST00000354233ENST00000461098HCFC1chrX

153214500

-HCFC1chrX

153214565

+
intron-intronENST00000369984ENST00000461098HCFC1chrX

153220827

+HCFC1chrX

153221692

-
intron-intronENST00000369984ENST00000461098HCFC1chrX

153214500

-HCFC1chrX

153214565

+
intron-intronENST00000461098ENST00000461098HCFC1chrX

153220827

+HCFC1chrX

153221692

-
intron-intronENST00000461098ENST00000461098HCFC1chrX

153214500

-HCFC1chrX

153214565

+

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 HCFC1-HCFC1


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)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

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.

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Fusion Protein Features for HCFC1-HCFC1


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/:153220827/:153221692)
- 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
HCFC1

P51610

HCFC1

Q9NWW0

FUNCTION: Involved in control of the cell cycle (PubMed:10629049, PubMed:10779346, PubMed:15190068, PubMed:16624878, PubMed:23629655). Also antagonizes transactivation by ZBTB17 and GABP2; represses ZBTB17 activation of the p15(INK4b) promoter and inhibits its ability to recruit p300 (PubMed:10675337, PubMed:12244100). Coactivator for EGR2 and GABP2 (PubMed:12244100, PubMed:14532282). Tethers the chromatin modifying Set1/Ash2 histone H3 'Lys-4' methyltransferase (H3K4me) and Sin3 histone deacetylase (HDAC) complexes (involved in the activation and repression of transcription, respectively) together (PubMed:12670868). Component of a THAP1/THAP3-HCFC1-OGT complex that is required for the regulation of the transcriptional activity of RRM1 (PubMed:20200153). As part of the NSL complex it may be involved in acetylation of nucleosomal histone H4 on several lysine residues (PubMed:20018852). Recruits KMT2E/MLL5 to E2F1 responsive promoters promoting transcriptional activation and thereby facilitates G1 to S phase transition (PubMed:23629655). {ECO:0000269|PubMed:10629049, ECO:0000269|PubMed:10675337, ECO:0000269|PubMed:10779346, ECO:0000269|PubMed:12244100, ECO:0000269|PubMed:12670868, ECO:0000269|PubMed:14532282, ECO:0000269|PubMed:15190068, ECO:0000269|PubMed:16624878, ECO:0000269|PubMed:20018852, ECO:0000269|PubMed:20200153, ECO:0000269|PubMed:23629655}.; FUNCTION: (Microbial infection) In case of human herpes simplex virus (HSV) infection, HCFC1 forms a multiprotein-DNA complex with the viral transactivator protein VP16 and POU2F1 thereby enabling the transcription of the viral immediate early genes. {ECO:0000269|PubMed:10629049, ECO:0000269|PubMed:17578910}.FUNCTION: Regulates HCFC1 activity by modulating its subcellular localization. Overexpression of HCFC1R1 leads to accumulation of HCFC1 in the cytoplasm. HCFC1R1-mediated export may provide the pool of cytoplasmic HCFC1 required for import of virion-derived VP16 into the nucleus. {ECO:0000269|PubMed:12235138}.

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 HCFC1-HCFC1


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 HCFC1-HCFC1


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 HCFC1-HCFC1


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 HCFC1-HCFC1


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