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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:KDM2A-PACS1 (FusionGDB2 ID:41537)

Fusion Gene Summary for KDM2A-PACS1

check button Fusion gene summary
Fusion gene informationFusion gene name: KDM2A-PACS1
Fusion gene ID: 41537
HgeneTgene
Gene symbol

KDM2A

PACS1

Gene ID

22992

55690

Gene namelysine demethylase 2Aphosphofurin acidic cluster sorting protein 1
SynonymsCXXC8|FBL11|FBL7|FBXL11|JHDM1A|LILINAMRD17|SHMS
Cytomap

11q13.2

11q13.1-q13.2

Type of geneprotein-codingprotein-coding
Descriptionlysine-specific demethylase 2ACXXC-type zinc finger protein 8F-box and leucine-rich repeat protein 11F-box/LRR-repeat protein 11[Histone-H3]-lysine-36 demethylase 1AjmjC domain-containing histone demethylation protein 1Ajumonji C domain-containing hphosphofurin acidic cluster sorting protein 1PACS-1cytosolic sorting protein PACS-1
Modification date2020032020200313
UniProtAcc

Q9Y2K7

.
Ensembl transtripts involved in fusion geneENST00000398645, ENST00000529006, 
ENST00000526258, ENST00000308783, 
ENST00000530342, 		ENST00000320580, 
ENST00000529757, ENST00000524815, 
Fusion gene scores* DoF score36 X 24 X 17=1468821 X 18 X 12=4536
# samples 5026
** MAII scorelog2(50/14688*10)=-4.87656605875172
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(26/4536*10)=-4.12483711191377
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: KDM2A [Title/Abstract] AND PACS1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointKDM2A(66888829)-PACS1(66010383), # samples:3
KDM2A(66888829)-PACS1(65960957), # samples:3
Anticipated loss of major functional domain due to fusion event.KDM2A-PACS1 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
KDM2A-PACS1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
KDM2A-PACS1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
KDM2A-PACS1 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
KDM2A-PACS1 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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

check buttonFusion gene breakpoints across KDM2A (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 PACS1 (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-B0-5713-01AKDM2Achr11

66888829

+PACS1chr11

66010383

+
ChimerDB4LUADTCGA-99-8025-01AKDM2Achr11

66888829

+PACS1chr11

65960957

+
ChimerDB4LUADTCGA-99-8025KDM2Achr11

66888829

+PACS1chr11

65960956

+
ChimerDB4KIRCTCGA-B0-5713-01AKDM2Achr11

66888829

+PACS1chr11

66010383

+
ChimerDB4LUADTCGA-99-8025-01AKDM2Achr11

66888829

+PACS1chr11

65960957

+
ChimerDB4LUADTCGA-99-8025-01AKDM2Achr11

66888829

-PACS1chr11

65960957

+
ChimerDB4KIRCTCGA-B0-5713-01AKDM2Achr11

66888829

-PACS1chr11

66010383

+


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Fusion Gene ORF analysis for KDM2A-PACS1

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-shiftENST00000398645ENST00000320580KDM2Achr11

66888829

+PACS1chr11

66010383

+
Frame-shiftENST00000398645ENST00000529757KDM2Achr11

66888829

+PACS1chr11

66010383

+
Frame-shiftENST00000398645ENST00000524815KDM2Achr11

66888829

+PACS1chr11

66010383

+
Frame-shiftENST00000529006ENST00000320580KDM2Achr11

66888829

+PACS1chr11

66010383

+
Frame-shiftENST00000529006ENST00000529757KDM2Achr11

66888829

+PACS1chr11

66010383

+
Frame-shiftENST00000529006ENST00000524815KDM2Achr11

66888829

+PACS1chr11

66010383

+
intron-3CDSENST00000526258ENST00000320580KDM2Achr11

66888829

+PACS1chr11

66010383

+
intron-3CDSENST00000526258ENST00000529757KDM2Achr11

66888829

+PACS1chr11

66010383

+
intron-3CDSENST00000526258ENST00000524815KDM2Achr11

66888829

+PACS1chr11

66010383

+
intron-3CDSENST00000308783ENST00000320580KDM2Achr11

66888829

+PACS1chr11

66010383

+
intron-3CDSENST00000308783ENST00000529757KDM2Achr11

66888829

+PACS1chr11

66010383

+
intron-3CDSENST00000308783ENST00000524815KDM2Achr11

66888829

+PACS1chr11

66010383

+
intron-3CDSENST00000530342ENST00000320580KDM2Achr11

66888829

+PACS1chr11

66010383

+
intron-3CDSENST00000530342ENST00000529757KDM2Achr11

66888829

+PACS1chr11

66010383

+
intron-3CDSENST00000530342ENST00000524815KDM2Achr11

66888829

+PACS1chr11

66010383

+
Frame-shiftENST00000398645ENST00000320580KDM2Achr11

66888829

+PACS1chr11

65960957

+
5CDS-intronENST00000398645ENST00000529757KDM2Achr11

66888829

+PACS1chr11

65960957

+
5CDS-intronENST00000398645ENST00000524815KDM2Achr11

66888829

+PACS1chr11

65960957

+
Frame-shiftENST00000529006ENST00000320580KDM2Achr11

66888829

+PACS1chr11

65960957

+
5CDS-intronENST00000529006ENST00000529757KDM2Achr11

66888829

+PACS1chr11

65960957

+
5CDS-intronENST00000529006ENST00000524815KDM2Achr11

66888829

+PACS1chr11

65960957

+
intron-3CDSENST00000526258ENST00000320580KDM2Achr11

66888829

+PACS1chr11

65960957

+
intron-intronENST00000526258ENST00000529757KDM2Achr11

66888829

+PACS1chr11

65960957

+
intron-intronENST00000526258ENST00000524815KDM2Achr11

66888829

+PACS1chr11

65960957

+
intron-3CDSENST00000308783ENST00000320580KDM2Achr11

66888829

+PACS1chr11

65960957

+
intron-intronENST00000308783ENST00000529757KDM2Achr11

66888829

+PACS1chr11

65960957

+
intron-intronENST00000308783ENST00000524815KDM2Achr11

66888829

+PACS1chr11

65960957

+
intron-3CDSENST00000530342ENST00000320580KDM2Achr11

66888829

+PACS1chr11

65960957

+
intron-intronENST00000530342ENST00000529757KDM2Achr11

66888829

+PACS1chr11

65960957

+
intron-intronENST00000530342ENST00000524815KDM2Achr11

66888829

+PACS1chr11

65960957

+
Frame-shiftENST00000398645ENST00000320580KDM2Achr11

66888829

+PACS1chr11

65960956

+
5CDS-intronENST00000398645ENST00000529757KDM2Achr11

66888829

+PACS1chr11

65960956

+
5CDS-intronENST00000398645ENST00000524815KDM2Achr11

66888829

+PACS1chr11

65960956

+
Frame-shiftENST00000529006ENST00000320580KDM2Achr11

66888829

+PACS1chr11

65960956

+
5CDS-intronENST00000529006ENST00000529757KDM2Achr11

66888829

+PACS1chr11

65960956

+
5CDS-intronENST00000529006ENST00000524815KDM2Achr11

66888829

+PACS1chr11

65960956

+
intron-3CDSENST00000526258ENST00000320580KDM2Achr11

66888829

+PACS1chr11

65960956

+
intron-intronENST00000526258ENST00000529757KDM2Achr11

66888829

+PACS1chr11

65960956

+
intron-intronENST00000526258ENST00000524815KDM2Achr11

66888829

+PACS1chr11

65960956

+
intron-3CDSENST00000308783ENST00000320580KDM2Achr11

66888829

+PACS1chr11

65960956

+
intron-intronENST00000308783ENST00000529757KDM2Achr11

66888829

+PACS1chr11

65960956

+
intron-intronENST00000308783ENST00000524815KDM2Achr11

66888829

+PACS1chr11

65960956

+
intron-3CDSENST00000530342ENST00000320580KDM2Achr11

66888829

+PACS1chr11

65960956

+
intron-intronENST00000530342ENST00000529757KDM2Achr11

66888829

+PACS1chr11

65960956

+
intron-intronENST00000530342ENST00000524815KDM2Achr11

66888829

+PACS1chr11

65960956

+

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 KDM2A-PACS1


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)
KDM2Achr1166888829+PACS1chr1166010382+5.68E-060.9999943
KDM2Achr1166888829+PACS1chr1165960956+7.94E-111
KDM2Achr1166888829+PACS1chr1165960956+7.94E-111
KDM2Achr1166888829+PACS1chr1166010382+5.68E-060.9999943
KDM2Achr1166888829+PACS1chr1165960956+7.94E-111
KDM2Achr1166888829+PACS1chr1165960956+7.94E-111

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 KDM2A-PACS1


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
KDM2A

Q9Y2K7

.
FUNCTION: Histone demethylase that specifically demethylates 'Lys-36' of histone H3, thereby playing a central role in histone code. Preferentially demethylates dimethylated H3 'Lys-36' residue while it has weak or no activity for mono- and tri-methylated H3 'Lys-36'. May also recognize and bind to some phosphorylated proteins and promote their ubiquitination and degradation. Required to maintain the heterochromatic state. Associates with centromeres and represses transcription of small non-coding RNAs that are encoded by the clusters of satellite repeats at the centromere. Required to sustain centromeric integrity and genomic stability, particularly during mitosis. Regulates circadian gene expression by repressing the transcriptional activator activity of CLOCK-ARNTL/BMAL1 heterodimer and RORA in a catalytically-independent manner (PubMed:26037310). {ECO:0000269|PubMed:16362057, ECO:0000269|PubMed:19001877, ECO:0000269|PubMed:26037310, 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 KDM2A-PACS1


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 KDM2A-PACS1


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 KDM2A-PACS1


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 KDM2A-PACS1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneKDM2AC0009402Colorectal Carcinoma1CTD_human
HgeneKDM2AC0009404Colorectal Neoplasms1CTD_human
HgeneKDM2AC2931456Prostate cancer, familial1CTD_human
HgeneKDM2AC4722327PROSTATE CANCER, HEREDITARY, 11CTD_human
TgenePACS1C3714756Intellectual Disability2GENOMICS_ENGLAND
TgenePACS1C0005586Bipolar Disorder1CTD_human
TgenePACS1C0005587Depression, Bipolar1CTD_human
TgenePACS1C0013146Drug abuse1CTD_human
TgenePACS1C0013170Drug habituation1CTD_human
TgenePACS1C0013222Drug Use Disorders1CTD_human
TgenePACS1C0024713Manic Disorder1CTD_human
TgenePACS1C0028754Obesity1CTD_human
TgenePACS1C0029231Organic Mental Disorders, Substance-Induced1CTD_human
TgenePACS1C0038580Substance Dependence1CTD_human
TgenePACS1C0038586Substance Use Disorders1CTD_human
TgenePACS1C0236969Substance-Related Disorders1CTD_human
TgenePACS1C0338831Manic1CTD_human
TgenePACS1C0740858Substance abuse problem1CTD_human
TgenePACS1C1510472Drug Dependence1CTD_human
TgenePACS1C3554343MENTAL RETARDATION, AUTOSOMAL DOMINANT 171GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgenePACS1C4316881Prescription Drug Abuse1CTD_human