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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:KDM2B-LRRIQ1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: KDM2B-LRRIQ1
FusionPDB ID: 41750
FusionGDB2.0 ID: 41750
HgeneTgene
Gene symbol

KDM2B

LRRIQ1

Gene ID

84678

84125

Gene namelysine demethylase 2Bleucine rich repeats and IQ motif containing 1
SynonymsCXXC2|FBXL10|Fbl10|JHDM1B|PCCX2-
Cytomap

12q24.31

12q21.31

Type of geneprotein-codingprotein-coding
Descriptionlysine-specific demethylase 2BCXXC-type zinc finger protein 2F-box and leucine-rich repeat protein 10F-box protein FBL10F-box/LRR-repeat protein 10JEMMA (Jumonji domain, EMSY-interactor, methyltransferase motif) protein[Histone-H3]-lysine-36 demethyleucine-rich repeat and IQ domain-containing protein 1testicular tissue protein Li 111
Modification date2020031320200320
UniProtAcc

Q8NHM5

Q96JM4

Ensembl transtripts involved in fusion geneENST idsENST00000377069, ENST00000377071, 
ENST00000536437, ENST00000538046, 
ENST00000542973, ENST00000543852, 
ENST00000528777, ENST00000393217, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score13 X 11 X 9=12878 X 8 X 5=320
# samples 1510
** MAII scorelog2(15/1287*10)=-3.10097764772482
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/320*10)=-1.67807190511264
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: KDM2B [Title/Abstract] AND LRRIQ1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)KDM2B(122012452)-LRRIQ1(85638567), # samples:3
Anticipated loss of major functional domain due to fusion event.KDM2B-LRRIQ1 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.
KDM2B-LRRIQ1 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.
KDM2B-LRRIQ1 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
KDM2B-LRRIQ1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
KDM2B-LRRIQ1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
KDM2B-LRRIQ1 seems lost the major protein functional domain in Hgene 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
HgeneKDM2B

GO:0035518

histone H2A monoubiquitination

16943429

HgeneKDM2B

GO:0070544

histone H3-K36 demethylation

26237645


check buttonFusion gene breakpoints across KDM2B (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 LRRIQ1 (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
ChimerDB4SARCTCGA-DX-A3LS-01AKDM2Bchr12

122012452

-LRRIQ1chr12

85638567

+


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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)
ENST00000377069KDM2Bchr12122012452-ENST00000393217LRRIQ1chr1285638567+1028711386835149
ENST00000377071KDM2Bchr12122012452-ENST00000393217LRRIQ1chr1285638567+78747073594173
ENST00000538046KDM2Bchr12122012452-ENST00000393217LRRIQ1chr1285638567+818501104625173

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
ENST00000377069ENST00000393217KDM2Bchr12122012452-LRRIQ1chr1285638567+0.0100806940.9899193
ENST00000377071ENST00000393217KDM2Bchr12122012452-LRRIQ1chr1285638567+0.0029963810.9970036
ENST00000538046ENST00000393217KDM2Bchr12122012452-LRRIQ1chr1285638567+0.0026965750.99730337

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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

>41750_41750_1_KDM2B-LRRIQ1_KDM2B_chr12_122012452_ENST00000377069_LRRIQ1_chr12_85638567_ENST00000393217_length(amino acids)=149AA_BP=105
MVNSPKKMEAEKDSGRRLRPIDRQRYDENEDLSDVEEIVSVRGFSLEEKLRSQLYQGDFVHAMEGKDFNYEYVQREALRVPLIFREKDGL

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

>41750_41750_2_KDM2B-LRRIQ1_KDM2B_chr12_122012452_ENST00000377071_LRRIQ1_chr12_85638567_ENST00000393217_length(amino acids)=173AA_BP=129
MAGPQMGGSAEDHPPRKRHAAEKQKKKTVIYTKCFEFESATQRPIDRQRYDENEDLSDVEEIVSVRGFSLEEKLRSQLYQGDFVHAMEGK

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

>41750_41750_3_KDM2B-LRRIQ1_KDM2B_chr12_122012452_ENST00000538046_LRRIQ1_chr12_85638567_ENST00000393217_length(amino acids)=173AA_BP=129
MAGPQMGGSAEDHPPRKRHAAEKQKKKTVIYTKCFEFESATQRPIDRQRYDENEDLSDVEEIVSVRGFSLEEKLRSQLYQGDFVHAMEGK

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

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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/chr12:122012452/chr12:85638567)
- 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
KDM2B

Q8NHM5

LRRIQ1

Q96JM4

FUNCTION: Histone demethylase that demethylates 'Lys-4' and 'Lys-36' of histone H3, thereby playing a central role in histone code (PubMed:16362057, PubMed:17994099, PubMed:26237645). Preferentially demethylates trimethylated H3 'Lys-4' and dimethylated H3 'Lys-36' residue while it has weak or no activity for mono- and tri-methylated H3 'Lys-36' (PubMed:16362057, PubMed:17994099, PubMed:26237645). Preferentially binds the transcribed region of ribosomal RNA and represses the transcription of ribosomal RNA genes which inhibits cell growth and proliferation (PubMed:16362057, PubMed:17994099). May also serve as a substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex (Probable). {ECO:0000269|PubMed:16362057, ECO:0000269|PubMed:17994099, ECO:0000269|PubMed:26237645, ECO:0000305}.

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

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377069-423943_971101.333333333333331266.0Coiled coilOntology_term=ECO:0000255
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377071-423943_971132.333333333333341337.0Coiled coilOntology_term=ECO:0000255
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000542973-114943_9710912.0Coiled coilOntology_term=ECO:0000255
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377069-4231014_1056101.333333333333331266.0Compositional biasNote=Pro-rich
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377069-423409_430101.333333333333331266.0Compositional biasNote=Glu-rich
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377071-4231014_1056132.333333333333341337.0Compositional biasNote=Pro-rich
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377071-423409_430132.333333333333341337.0Compositional biasNote=Glu-rich
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000542973-1141014_10560912.0Compositional biasNote=Pro-rich
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000542973-114409_4300912.0Compositional biasNote=Glu-rich
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377069-4231059_1105101.333333333333331266.0DomainNote=F-box
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377069-423178_346101.333333333333331266.0DomainJmjC
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377071-4231059_1105132.333333333333341337.0DomainNote=F-box
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377071-423178_346132.333333333333341337.0DomainJmjC
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000542973-1141059_11050912.0DomainNote=F-box
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000542973-114178_3460912.0DomainJmjC
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377069-4231093_1120101.333333333333331266.0RepeatNote=LRR 1
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377069-4231133_1154101.333333333333331266.0RepeatNote=LRR 2
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377069-4231156_1182101.333333333333331266.0RepeatNote=LRR 3
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377069-4231222_1247101.333333333333331266.0RepeatNote=LRR 4
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377069-4231248_1277101.333333333333331266.0RepeatNote=LRR 5
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377069-4231278_1302101.333333333333331266.0RepeatNote=LRR 6
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377069-4231303_1336101.333333333333331266.0RepeatNote=LRR 7
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377071-4231093_1120132.333333333333341337.0RepeatNote=LRR 1
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377071-4231133_1154132.333333333333341337.0RepeatNote=LRR 2
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377071-4231156_1182132.333333333333341337.0RepeatNote=LRR 3
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377071-4231222_1247132.333333333333341337.0RepeatNote=LRR 4
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377071-4231248_1277132.333333333333341337.0RepeatNote=LRR 5
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377071-4231278_1302132.333333333333341337.0RepeatNote=LRR 6
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377071-4231303_1336132.333333333333341337.0RepeatNote=LRR 7
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000542973-1141093_11200912.0RepeatNote=LRR 1
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000542973-1141133_11540912.0RepeatNote=LRR 2
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000542973-1141156_11820912.0RepeatNote=LRR 3
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000542973-1141222_12470912.0RepeatNote=LRR 4
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000542973-1141248_12770912.0RepeatNote=LRR 5
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000542973-1141278_13020912.0RepeatNote=LRR 6
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000542973-1141303_13360912.0RepeatNote=LRR 7
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377069-423606_652101.333333333333331266.0Zinc fingerCXXC-type
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377069-423659_725101.333333333333331266.0Zinc fingerPHD-type
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377071-423606_652132.333333333333341337.0Zinc fingerCXXC-type
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000377071-423659_725132.333333333333341337.0Zinc fingerPHD-type
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000542973-114606_6520912.0Zinc fingerCXXC-type
HgeneKDM2Bchr12:122012452chr12:85638567ENST00000542973-114659_7250912.0Zinc fingerPHD-type
TgeneLRRIQ1chr12:122012452chr12:85638567ENST000003932172527162_3761672.01723.0Compositional biasNote=Glu-rich
TgeneLRRIQ1chr12:122012452chr12:85638567ENST0000039321725271117_11571672.01723.0DomainNote=LRRCT
TgeneLRRIQ1chr12:122012452chr12:85638567ENST0000039321725271335_13641672.01723.0DomainIQ 2
TgeneLRRIQ1chr12:122012452chr12:85638567ENST0000039321725271395_14241672.01723.0DomainIQ 3
TgeneLRRIQ1chr12:122012452chr12:85638567ENST000003932172527283_3121672.01723.0DomainIQ 1
TgeneLRRIQ1chr12:122012452chr12:85638567ENST0000039321725271014_10351672.01723.0RepeatNote=LRR 7
TgeneLRRIQ1chr12:122012452chr12:85638567ENST0000039321725271036_10571672.01723.0RepeatNote=LRR 8
TgeneLRRIQ1chr12:122012452chr12:85638567ENST0000039321725271060_10811672.01723.0RepeatNote=LRR 9
TgeneLRRIQ1chr12:122012452chr12:85638567ENST0000039321725271082_11031672.01723.0RepeatNote=LRR 10
TgeneLRRIQ1chr12:122012452chr12:85638567ENST000003932172527819_8401672.01723.0RepeatNote=LRR 1
TgeneLRRIQ1chr12:122012452chr12:85638567ENST000003932172527841_8611672.01723.0RepeatNote=LRR 2
TgeneLRRIQ1chr12:122012452chr12:85638567ENST000003932172527862_8831672.01723.0RepeatNote=LRR 3
TgeneLRRIQ1chr12:122012452chr12:85638567ENST000003932172527884_9051672.01723.0RepeatNote=LRR 4
TgeneLRRIQ1chr12:122012452chr12:85638567ENST000003932172527970_9911672.01723.0RepeatNote=LRR 5
TgeneLRRIQ1chr12:122012452chr12:85638567ENST000003932172527992_10131672.01723.0RepeatNote=LRR 6


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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
KDM2B
LRRIQ1


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 KDM2B-LRRIQ1


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 KDM2B-LRRIQ1


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