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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:KDM4C-RFX3 (FusionGDB2 ID:41653)

Fusion Gene Summary for KDM4C-RFX3

check button Fusion gene summary
Fusion gene informationFusion gene name: KDM4C-RFX3
Fusion gene ID: 41653
HgeneTgene
Gene symbol

KDM4C

RFX3

Gene ID

23081

5991

Gene namelysine demethylase 4Cregulatory factor X3
SynonymsGASC1|JHDM3C|JMJD2C|TDRD14C-
Cytomap

9p24.1

9p24.2

Type of geneprotein-codingprotein-coding
Descriptionlysine-specific demethylase 4CJmjC domain-containing histone demethylation protein 3Cgene amplified in squamous cell carcinoma 1 proteinjumonji domain-containing protein 2Clysine (K)-specific demethylase 4Ctudor domain containing 14Ctranscription factor RFX3DNA binding protein RFX3regulatory factor X, 3 (influences HLA class II expression)
Modification date2020032920200327
UniProtAcc

Q9H3R0

.
Ensembl transtripts involved in fusion geneENST00000535193, ENST00000543771, 
ENST00000381306, ENST00000381309, 
ENST00000442236, ENST00000489243, 
ENST00000536108, ENST00000428870, 
ENST00000401787, 		ENST00000382004, 
ENST00000358730, ENST00000302303, 
ENST00000381984, 
Fusion gene scores* DoF score22 X 15 X 12=396010 X 10 X 4=400
# samples 229
** MAII scorelog2(22/3960*10)=-4.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/400*10)=-2.15200309344505
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: KDM4C [Title/Abstract] AND RFX3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointKDM4C(6805774)-RFX3(3225280), # samples:3
Anticipated loss of major functional domain due to fusion event.KDM4C-RFX3 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
KDM4C-RFX3 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
KDM4C-RFX3 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
KDM4C-RFX3 seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted 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
HgeneKDM4C

GO:0006357

regulation of transcription by RNA polymerase II

17277772

HgeneKDM4C

GO:0033169

histone H3-K9 demethylation

18066052|21914792

HgeneKDM4C

GO:0070544

histone H3-K36 demethylation

21914792

TgeneRFX3

GO:0045892

negative regulation of transcription, DNA-templated

12411430

TgeneRFX3

GO:0045893

positive regulation of transcription, DNA-templated

20148032


check buttonFusion gene breakpoints across KDM4C (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 RFX3 (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
ChimerDB4KIRCTCGA-B0-4696-01AKDM4Cchr9

6805774

+RFX3chr9

3225280

-
ChimerDB4KIRCTCGA-B0-4696-01AKDM4Cchr9

6805774

+RFX3chr9

3225280

-
ChimerDB4KIRCTCGA-B0-4696-01AKDM4Cchr9

6805774

-RFX3chr9

3225280

-


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Fusion Gene ORF analysis for KDM4C-RFX3

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-shiftENST00000535193ENST00000382004KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000535193ENST00000358730KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000535193ENST00000302303KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000535193ENST00000381984KDM4Cchr9

6805774

+RFX3chr9

3225280

-
Frame-shiftENST00000543771ENST00000382004KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000543771ENST00000358730KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000543771ENST00000302303KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000543771ENST00000381984KDM4Cchr9

6805774

+RFX3chr9

3225280

-
Frame-shiftENST00000381306ENST00000382004KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000381306ENST00000358730KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000381306ENST00000302303KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000381306ENST00000381984KDM4Cchr9

6805774

+RFX3chr9

3225280

-
Frame-shiftENST00000381309ENST00000382004KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000381309ENST00000358730KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000381309ENST00000302303KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000381309ENST00000381984KDM4Cchr9

6805774

+RFX3chr9

3225280

-
intron-3CDSENST00000442236ENST00000382004KDM4Cchr9

6805774

+RFX3chr9

3225280

-
intron-intronENST00000442236ENST00000358730KDM4Cchr9

6805774

+RFX3chr9

3225280

-
intron-intronENST00000442236ENST00000302303KDM4Cchr9

6805774

+RFX3chr9

3225280

-
intron-intronENST00000442236ENST00000381984KDM4Cchr9

6805774

+RFX3chr9

3225280

-
3UTR-3CDSENST00000489243ENST00000382004KDM4Cchr9

6805774

+RFX3chr9

3225280

-
3UTR-intronENST00000489243ENST00000358730KDM4Cchr9

6805774

+RFX3chr9

3225280

-
3UTR-intronENST00000489243ENST00000302303KDM4Cchr9

6805774

+RFX3chr9

3225280

-
3UTR-intronENST00000489243ENST00000381984KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5UTR-3CDSENST00000536108ENST00000382004KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5UTR-intronENST00000536108ENST00000358730KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5UTR-intronENST00000536108ENST00000302303KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5UTR-intronENST00000536108ENST00000381984KDM4Cchr9

6805774

+RFX3chr9

3225280

-
intron-3CDSENST00000428870ENST00000382004KDM4Cchr9

6805774

+RFX3chr9

3225280

-
intron-intronENST00000428870ENST00000358730KDM4Cchr9

6805774

+RFX3chr9

3225280

-
intron-intronENST00000428870ENST00000302303KDM4Cchr9

6805774

+RFX3chr9

3225280

-
intron-intronENST00000428870ENST00000381984KDM4Cchr9

6805774

+RFX3chr9

3225280

-
Frame-shiftENST00000401787ENST00000382004KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000401787ENST00000358730KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000401787ENST00000302303KDM4Cchr9

6805774

+RFX3chr9

3225280

-
5CDS-intronENST00000401787ENST00000381984KDM4Cchr9

6805774

+RFX3chr9

3225280

-

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 KDM4C-RFX3


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 KDM4C-RFX3


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
KDM4C

Q9H3R0

.
FUNCTION: Histone demethylase that specifically demethylates 'Lys-9' and 'Lys-36' residues of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27' nor H4 'Lys-20'. Demethylates trimethylated H3 'Lys-9' and H3 'Lys-36' residue, while it has no activity on mono- and dimethylated residues. Demethylation of Lys residue generates formaldehyde and succinate. {ECO:0000269|PubMed:16603238, ECO:0000269|PubMed:28262558}.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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 KDM4C-RFX3


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 KDM4C-RFX3


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 KDM4C-RFX3


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 KDM4C-RFX3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneKDM4CC0004565Melanoma, B161CTD_human
HgeneKDM4CC0009075Melanoma, Cloudman S911CTD_human
HgeneKDM4CC0018598Melanoma, Harding-Passey1CTD_human
HgeneKDM4CC0025149Medulloblastoma1CTD_human
HgeneKDM4CC0025202melanoma1CTD_human
HgeneKDM4CC0025205Melanoma, Experimental1CTD_human
HgeneKDM4CC0079772T-Cell Lymphoma1CTD_human
HgeneKDM4CC0205833Medullomyoblastoma1CTD_human
HgeneKDM4CC0236663Alcohol withdrawal syndrome1PSYGENET
HgeneKDM4CC0278510Childhood Medulloblastoma1CTD_human
HgeneKDM4CC0278876Adult Medulloblastoma1CTD_human
HgeneKDM4CC0751291Desmoplastic Medulloblastoma1CTD_human
HgeneKDM4CC1275668Melanotic medulloblastoma1CTD_human
TgeneRFX3C0037274Dermatologic disorders1CTD_human
TgeneRFX3C0274861Arsenic Poisoning, Inorganic1CTD_human
TgeneRFX3C0274862Nervous System, Organic Arsenic Poisoning1CTD_human
TgeneRFX3C0311375Arsenic Poisoning1CTD_human
TgeneRFX3C0751851Arsenic Encephalopathy1CTD_human
TgeneRFX3C0751852Arsenic Induced Polyneuropathy1CTD_human