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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:KDM2A-NIPAL3

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: KDM2A-NIPAL3
FusionPDB ID: 41726
FusionGDB2.0 ID: 41726
HgeneTgene
Gene symbol

KDM2A

NIPAL3

Gene ID

22992

57185

Gene namelysine demethylase 2ANIPA like domain containing 3
SynonymsCXXC8|FBL11|FBL7|FBXL11|JHDM1A|LILINADJ462O23.2|NPAL3
Cytomap

11q13.2

1p36.11

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 hNIPA-like protein 3
Modification date2020032020200313
UniProtAcc

Q9Y2K7

Q6P499

Ensembl transtripts involved in fusion geneENST idsENST00000398645, ENST00000529006, 
ENST00000308783, ENST00000526258, 
ENST00000530342, 		ENST00000003912, 
ENST00000339255, ENST00000358028, 
ENST00000428131, ENST00000488155, 
ENST00000374399, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score36 X 24 X 17=146887 X 8 X 5=280
# samples 507
** MAII scorelog2(50/14688*10)=-4.87656605875172
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/280*10)=-2
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: KDM2A [Title/Abstract] AND NIPAL3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)KDM2A(66888829)-NIPAL3(24766661), # samples:1
Anticipated loss of major functional domain due to fusion event.KDM2A-NIPAL3 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
KDM2A-NIPAL3 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
KDM2A-NIPAL3 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
KDM2A-NIPAL3 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame 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.
all structure

check buttonFusion gene breakpoints across NIPAL3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4THCATCGA-EM-A3SUKDM2Achr11

66888829

+NIPAL3chr1

24766661

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000398645KDM2Achr1166888829+ENST00000374399NIPAL3chr124766661+21569068642033389
ENST00000529006KDM2Achr1166888829+ENST00000374399NIPAL3chr124766661+17384884461615389

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
ENST00000398645ENST00000374399KDM2Achr1166888829+NIPAL3chr124766661+0.0033447090.9966552
ENST00000529006ENST00000374399KDM2Achr1166888829+NIPAL3chr124766661+0.0036000760.9963999

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>41726_41726_1_KDM2A-NIPAL3_KDM2A_chr11_66888829_ENST00000398645_NIPAL3_chr1_24766661_ENST00000374399_length(amino acids)=389AA_BP=14
MEPEEERIRYSQRLENLIGALLAIFGHLVVSIALNLQKYCHIRLAGSKDPRAYFKTKTWWLGLFLMLLGELGVFASYAFAPLSLIVPLSA
VSVIASAIIGIIFIKEKWKPKDFLRRYVLSFVGCGLAVVGTYLLVTFAPNSHEKMTGENVTRHLVSWPFLLYMLVEIILFCLLLYFYKEK
NANNIVVILLLVALLGSMTVVTVKAVAGMLVLSIQGNLQLDYPIFYVMFVCMVATAVYQAAFLSQASQMYDSSLIASVGYILSTTIAITA
GAIFYLDFIGEDVLHICMFALGCLIAFLGVFLITRNRKKPIPFEPYISMDAMPGMQNMHDKGMTVQPELKASFSYGALENNDNISEIYAP

--------------------------------------------------------------

>41726_41726_2_KDM2A-NIPAL3_KDM2A_chr11_66888829_ENST00000529006_NIPAL3_chr1_24766661_ENST00000374399_length(amino acids)=389AA_BP=14
MEPEEERIRYSQRLENLIGALLAIFGHLVVSIALNLQKYCHIRLAGSKDPRAYFKTKTWWLGLFLMLLGELGVFASYAFAPLSLIVPLSA
VSVIASAIIGIIFIKEKWKPKDFLRRYVLSFVGCGLAVVGTYLLVTFAPNSHEKMTGENVTRHLVSWPFLLYMLVEIILFCLLLYFYKEK
NANNIVVILLLVALLGSMTVVTVKAVAGMLVLSIQGNLQLDYPIFYVMFVCMVATAVYQAAFLSQASQMYDSSLIASVGYILSTTIAITA
GAIFYLDFIGEDVLHICMFALGCLIAFLGVFLITRNRKKPIPFEPYISMDAMPGMQNMHDKGMTVQPELKASFSYGALENNDNISEIYAP

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Fusion Protein Functional Features


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/chr11:66888829/chr1:24766661)
- 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
KDM2A

Q9Y2K7

NIPAL3

Q6P499

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}.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneNIPAL3chr11:66888829chr1:24766661ENST0000000391221318_210325.0Compositional biasNote=Poly-Ser
TgeneNIPAL3chr11:66888829chr1:24766661ENST00000003912213101_1210325.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST00000003912213135_1550325.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST00000003912213171_1910325.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST00000003912213202_2220325.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST00000003912213240_2600325.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST00000003912213271_2910325.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST00000003912213300_3200325.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST0000000391221333_530325.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST0000000391221376_960325.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST0000035802818101_12131.0227.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST0000035802818135_15531.0227.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST0000035802818171_19131.0227.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST0000035802818202_22231.0227.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST0000035802818240_26031.0227.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST0000035802818271_29131.0227.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST0000035802818300_32031.0227.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST000003580281833_5331.0227.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST000003580281876_9631.0227.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST00000374399112101_12131.0407.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST00000374399112135_15531.0407.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST00000374399112171_19131.0407.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST00000374399112202_22231.0407.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST00000374399112240_26031.0407.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST00000374399112271_29131.0407.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST00000374399112300_32031.0407.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST0000037439911233_5331.0407.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST0000037439911276_9631.0407.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST0000042813107101_12131.0227.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST0000042813107135_15531.0227.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST0000042813107171_19131.0227.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST0000042813107202_22231.0227.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST0000042813107240_26031.0227.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST0000042813107271_29131.0227.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST0000042813107300_32031.0227.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST000004281310733_5331.0227.0TransmembraneHelical
TgeneNIPAL3chr11:66888829chr1:24766661ENST000004281310776_9631.0227.0TransmembraneHelical

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneKDM2Achr11:66888829chr1:24766661ENST00000308783+110148_3160621.0DomainJmjC
HgeneKDM2Achr11:66888829chr1:24766661ENST00000308783+110889_9360621.0DomainNote=F-box
HgeneKDM2Achr11:66888829chr1:24766661ENST00000398645+221148_31614.01490.3333333333333DomainJmjC
HgeneKDM2Achr11:66888829chr1:24766661ENST00000398645+221889_93614.01490.3333333333333DomainNote=F-box
HgeneKDM2Achr11:66888829chr1:24766661ENST00000529006+221148_31614.01163.0DomainJmjC
HgeneKDM2Achr11:66888829chr1:24766661ENST00000529006+221889_93614.01163.0DomainNote=F-box
HgeneKDM2Achr11:66888829chr1:24766661ENST00000530342+110148_3160724.0DomainJmjC
HgeneKDM2Achr11:66888829chr1:24766661ENST00000530342+110889_9360724.0DomainNote=F-box
HgeneKDM2Achr11:66888829chr1:24766661ENST00000308783+1101048_10730621.0RepeatNote=LRR 3
HgeneKDM2Achr11:66888829chr1:24766661ENST00000308783+1101074_11030621.0RepeatNote=LRR 4
HgeneKDM2Achr11:66888829chr1:24766661ENST00000308783+1101104_11280621.0RepeatNote=LRR 5
HgeneKDM2Achr11:66888829chr1:24766661ENST00000308783+1101129_11560621.0RepeatNote=LRR 6
HgeneKDM2Achr11:66888829chr1:24766661ENST00000308783+110961_9820621.0RepeatNote=LRR 1
HgeneKDM2Achr11:66888829chr1:24766661ENST00000308783+110984_10100621.0RepeatNote=LRR 2
HgeneKDM2Achr11:66888829chr1:24766661ENST00000398645+2211048_107314.01490.3333333333333RepeatNote=LRR 3
HgeneKDM2Achr11:66888829chr1:24766661ENST00000398645+2211074_110314.01490.3333333333333RepeatNote=LRR 4
HgeneKDM2Achr11:66888829chr1:24766661ENST00000398645+2211104_112814.01490.3333333333333RepeatNote=LRR 5
HgeneKDM2Achr11:66888829chr1:24766661ENST00000398645+2211129_115614.01490.3333333333333RepeatNote=LRR 6
HgeneKDM2Achr11:66888829chr1:24766661ENST00000398645+221961_98214.01490.3333333333333RepeatNote=LRR 1
HgeneKDM2Achr11:66888829chr1:24766661ENST00000398645+221984_101014.01490.3333333333333RepeatNote=LRR 2
HgeneKDM2Achr11:66888829chr1:24766661ENST00000529006+2211048_107314.01163.0RepeatNote=LRR 3
HgeneKDM2Achr11:66888829chr1:24766661ENST00000529006+2211074_110314.01163.0RepeatNote=LRR 4
HgeneKDM2Achr11:66888829chr1:24766661ENST00000529006+2211104_112814.01163.0RepeatNote=LRR 5
HgeneKDM2Achr11:66888829chr1:24766661ENST00000529006+2211129_115614.01163.0RepeatNote=LRR 6
HgeneKDM2Achr11:66888829chr1:24766661ENST00000529006+221961_98214.01163.0RepeatNote=LRR 1
HgeneKDM2Achr11:66888829chr1:24766661ENST00000529006+221984_101014.01163.0RepeatNote=LRR 2
HgeneKDM2Achr11:66888829chr1:24766661ENST00000530342+1101048_10730724.0RepeatNote=LRR 3
HgeneKDM2Achr11:66888829chr1:24766661ENST00000530342+1101074_11030724.0RepeatNote=LRR 4
HgeneKDM2Achr11:66888829chr1:24766661ENST00000530342+1101104_11280724.0RepeatNote=LRR 5
HgeneKDM2Achr11:66888829chr1:24766661ENST00000530342+1101129_11560724.0RepeatNote=LRR 6
HgeneKDM2Achr11:66888829chr1:24766661ENST00000530342+110961_9820724.0RepeatNote=LRR 1
HgeneKDM2Achr11:66888829chr1:24766661ENST00000530342+110984_10100724.0RepeatNote=LRR 2
HgeneKDM2Achr11:66888829chr1:24766661ENST00000308783+110564_6100621.0Zinc fingerCXXC-type
HgeneKDM2Achr11:66888829chr1:24766661ENST00000308783+110617_6780621.0Zinc fingerPHD-type
HgeneKDM2Achr11:66888829chr1:24766661ENST00000398645+221564_61014.01490.3333333333333Zinc fingerCXXC-type
HgeneKDM2Achr11:66888829chr1:24766661ENST00000398645+221617_67814.01490.3333333333333Zinc fingerPHD-type
HgeneKDM2Achr11:66888829chr1:24766661ENST00000529006+221564_61014.01163.0Zinc fingerCXXC-type
HgeneKDM2Achr11:66888829chr1:24766661ENST00000529006+221617_67814.01163.0Zinc fingerPHD-type
HgeneKDM2Achr11:66888829chr1:24766661ENST00000530342+110564_6100724.0Zinc fingerCXXC-type
HgeneKDM2Achr11:66888829chr1:24766661ENST00000530342+110617_6780724.0Zinc fingerPHD-type
TgeneNIPAL3chr11:66888829chr1:24766661ENST000003580281818_2131.0227.0Compositional biasNote=Poly-Ser
TgeneNIPAL3chr11:66888829chr1:24766661ENST0000037439911218_2131.0407.0Compositional biasNote=Poly-Ser
TgeneNIPAL3chr11:66888829chr1:24766661ENST000004281310718_2131.0227.0Compositional biasNote=Poly-Ser


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
KDM2A
NIPAL3


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to KDM2A-NIPAL3


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to KDM2A-NIPAL3


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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