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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:HDAC1-LRRC42 (FusionGDB2 ID:35809)

Fusion Gene Summary for HDAC1-LRRC42

check button Fusion gene summary
Fusion gene informationFusion gene name: HDAC1-LRRC42
Fusion gene ID: 35809
HgeneTgene
Gene symbol

HDAC1

LRRC42

Gene ID

3065

115353

Gene namehistone deacetylase 1leucine rich repeat containing 42
SynonymsGON-10|HD1|KDAC1|RPD3|RPD3L1dJ167A19.4
Cytomap

1p35.2-p35.1

1p32.3

Type of geneprotein-codingprotein-coding
Descriptionhistone deacetylase 1reduced potassium dependency, yeast homolog-like 1leucine-rich repeat-containing protein 42
Modification date2020032720200313
UniProtAcc

Q13547

Q9Y546

Ensembl transtripts involved in fusion geneENST00000373548, ENST00000373541, 
ENST00000490081, 		ENST00000319223, 
ENST00000371370, ENST00000477905, 
Fusion gene scores* DoF score13 X 9 X 9=10533 X 5 X 3=45
# samples 175
** MAII scorelog2(17/1053*10)=-2.63089878488802
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/45*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: HDAC1 [Title/Abstract] AND LRRC42 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointHDAC1(32757819)-LRRC42(54417659), # samples:2
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
HgeneHDAC1

GO:0000122

negative regulation of transcription by RNA polymerase II

18854353

HgeneHDAC1

GO:0006476

protein deacetylation

17172643|23629966

HgeneHDAC1

GO:0045893

positive regulation of transcription, DNA-templated

16762839

HgeneHDAC1

GO:0045944

positive regulation of transcription by RNA polymerase II

16762839

HgeneHDAC1

GO:0060766

negative regulation of androgen receptor signaling pathway

15919722

HgeneHDAC1

GO:0070932

histone H3 deacetylation

12590135

HgeneHDAC1

GO:0070933

histone H4 deacetylation

12590135


check buttonFusion gene breakpoints across HDAC1 (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 LRRC42 (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
ChimerDB4LGGTCGA-HT-7860-01AHDAC1chr1

32757819

-LRRC42chr1

54417659

+
ChimerDB4LGGTCGA-HT-7860-01AHDAC1chr1

32757819

+LRRC42chr1

54417659

+
ChimerDB4LGGTCGA-HT-7860HDAC1chr1

32757819

+LRRC42chr1

54412122

+


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Fusion Gene ORF analysis for HDAC1-LRRC42

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
5CDS-5UTRENST00000373548ENST00000319223HDAC1chr1

32757819

+LRRC42chr1

54417659

+
5CDS-5UTRENST00000373548ENST00000319223HDAC1chr1

32757819

+LRRC42chr1

54412122

+
5CDS-5UTRENST00000373548ENST00000371370HDAC1chr1

32757819

+LRRC42chr1

54417659

+
5CDS-5UTRENST00000373548ENST00000371370HDAC1chr1

32757819

+LRRC42chr1

54412122

+
5CDS-intronENST00000373548ENST00000477905HDAC1chr1

32757819

+LRRC42chr1

54417659

+
5CDS-intronENST00000373548ENST00000477905HDAC1chr1

32757819

+LRRC42chr1

54412122

+
intron-5UTRENST00000373541ENST00000319223HDAC1chr1

32757819

+LRRC42chr1

54417659

+
intron-5UTRENST00000373541ENST00000319223HDAC1chr1

32757819

+LRRC42chr1

54412122

+
intron-5UTRENST00000373541ENST00000371370HDAC1chr1

32757819

+LRRC42chr1

54417659

+
intron-5UTRENST00000373541ENST00000371370HDAC1chr1

32757819

+LRRC42chr1

54412122

+
intron-5UTRENST00000490081ENST00000319223HDAC1chr1

32757819

+LRRC42chr1

54417659

+
intron-5UTRENST00000490081ENST00000319223HDAC1chr1

32757819

+LRRC42chr1

54412122

+
intron-5UTRENST00000490081ENST00000371370HDAC1chr1

32757819

+LRRC42chr1

54417659

+
intron-5UTRENST00000490081ENST00000371370HDAC1chr1

32757819

+LRRC42chr1

54412122

+
intron-intronENST00000373541ENST00000477905HDAC1chr1

32757819

+LRRC42chr1

54417659

+
intron-intronENST00000373541ENST00000477905HDAC1chr1

32757819

+LRRC42chr1

54412122

+
intron-intronENST00000490081ENST00000477905HDAC1chr1

32757819

+LRRC42chr1

54417659

+
intron-intronENST00000490081ENST00000477905HDAC1chr1

32757819

+LRRC42chr1

54412122

+

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 HDAC1-LRRC42


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)
HDAC1chr132757819+LRRC42chr154417658+4.04E-131
HDAC1chr132757819+LRRC42chr154417658+4.04E-131

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.
genomic feature of top 1%

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Fusion Protein Features for HDAC1-LRRC42


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/:32757819/:54417659)
- 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
HDAC1

Q13547

LRRC42

Q9Y546

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. Deacetylates SP proteins, SP1 and SP3, and regulates their function. Component of the BRG1-RB1-HDAC1 complex, which negatively regulates the CREST-mediated transcription in resting neurons. Upon calcium stimulation, HDAC1 is released from the complex and CREBBP is recruited, which facilitates transcriptional activation. Deacetylates TSHZ3 and regulates its transcriptional repressor activity. Deacetylates 'Lys-310' in RELA and thereby inhibits the transcriptional activity of NF-kappa-B. Deacetylates NR1D2 and abrogates the effect of KAT5-mediated relieving of NR1D2 transcription repression activity. Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development. Involved in CIART-mediated transcriptional repression of the circadian transcriptional activator: CLOCK-ARNTL/BMAL1 heterodimer. Required for the transcriptional repression of circadian target genes, such as PER1, mediated by the large PER complex or CRY1 through histone deacetylation. {ECO:0000269|PubMed:12837748, ECO:0000269|PubMed:16478997, ECO:0000269|PubMed:17000776, ECO:0000269|PubMed:17704056, ECO:0000269|PubMed:17996965, ECO:0000269|PubMed:19081374, ECO:0000269|PubMed:19343227}.

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 HDAC1-LRRC42


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 HDAC1-LRRC42


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 HDAC1-LRRC42


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 HDAC1-LRRC42


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