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Center for Computational Systems Medicine
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Fusion Gene and Fusion Protein Summary

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Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)

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Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)

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Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)

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Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)

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Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)

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Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)

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Potential target of CAR-T therapy development

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Information on the samples that have these potential fusion neoantigens

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Fusion Protein Targeting Drugs - (Manual Curation)

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Fusion Protein Related diseases - (Manual Curation)

Fusion Protein:KMT2A-MLLT10

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: KMT2A-MLLT10
FusionPDB ID: 43192
FusionGDB2.0 ID: 54242
HgeneTgene
Gene symbol

KMT2A

MLLT10

Gene ID

4297

8028

Gene namelysine methyltransferase 2AMLLT10 histone lysine methyltransferase DOT1L cofactor
SynonymsALL-1|CXXC7|HRX|HTRX1|MLL|MLL1|MLL1A|TRX1|WDSTSAF10
Cytomap

11q23.3

10p12.31

Type of geneprotein-codingprotein-coding
Descriptionhistone-lysine N-methyltransferase 2ACXXC-type zinc finger protein 7lysine (K)-specific methyltransferase 2Alysine N-methyltransferase 2Amixed lineage leukemia 1myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)trithorax-likeprotein AF-10ALL1-fused gene from chromosome 10 proteinmyeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10myeloid/lymphoid or mixed-lineage leukemia; translocated to, 10type I AF10 proteintype III AF10 prot
Modification date2020031920200313
UniProtAcc

Q03164

Main function of 5'-partner protein: FUNCTION: Histone methyltransferase that plays an essential role in early development and hematopoiesis (PubMed:15960975, PubMed:12453419, PubMed:15960975, PubMed:19556245, PubMed:19187761, PubMed:20677832, PubMed:21220120, PubMed:26886794). Catalytic subunit of the MLL1/MLL complex, a multiprotein complex that mediates both methylation of 'Lys-4' of histone H3 (H3K4me) complex and acetylation of 'Lys-16' of histone H4 (H4K16ac) (PubMed:15960975, PubMed:12453419, PubMed:15960975, PubMed:19556245, PubMed:24235145, PubMed:19187761, PubMed:20677832, PubMed:21220120, PubMed:26886794). Catalyzes methyl group transfer from S-adenosyl-L-methionine to the epsilon-amino group of 'Lys-4' of histone H3 (H3K4) via a non-processive mechanism. Part of chromatin remodeling machinery predominantly forms H3K4me1 and H3K4me2 methylation marks at active chromatin sites where transcription and DNA repair take place (PubMed:25561738, PubMed:15960975, PubMed:12453419, PubMed:15960975, PubMed:19556245, PubMed:19187761, PubMed:20677832, PubMed:21220120, PubMed:26886794). Has weak methyltransferase activity by itself, and requires other component of the MLL1/MLL complex to obtain full methyltransferase activity (PubMed:19187761, PubMed:26886794). Has no activity toward histone H3 phosphorylated on 'Thr-3', less activity toward H3 dimethylated on 'Arg-8' or 'Lys-9', while it has higher activity toward H3 acetylated on 'Lys-9' (PubMed:19187761). Binds to unmethylated CpG elements in the promoter of target genes and helps maintain them in the nonmethylated state (PubMed:20010842). Required for transcriptional activation of HOXA9 (PubMed:12453419, PubMed:20677832, PubMed:20010842). Promotes PPP1R15A-induced apoptosis (PubMed:10490642). Plays a critical role in the control of circadian gene expression and is essential for the transcriptional activation mediated by the CLOCK-ARNTL/BMAL1 heterodimer (By similarity). Establishes a permissive chromatin state for circadian transcription by mediating a rhythmic methylation of 'Lys-4' of histone H3 (H3K4me) and this histone modification directs the circadian acetylation at H3K9 and H3K14 allowing the recruitment of CLOCK-ARNTL/BMAL1 to chromatin (By similarity). Also has auto-methylation activity on Cys-3882 in absence of histone H3 substrate (PubMed:24235145). {ECO:0000250|UniProtKB:P55200, ECO:0000269|PubMed:10490642, ECO:0000269|PubMed:12453419, ECO:0000269|PubMed:15960975, ECO:0000269|PubMed:19187761, ECO:0000269|PubMed:19556245, ECO:0000269|PubMed:20010842, ECO:0000269|PubMed:21220120, ECO:0000269|PubMed:24235145, ECO:0000269|PubMed:26886794, ECO:0000305|PubMed:20677832}.

P55197

Main function of 5'-partner protein: FUNCTION: Probably involved in transcriptional regulation. In vitro or as fusion protein with KMT2A/MLL1 has transactivation activity. Binds to cruciform DNA. In cells, binding to unmodified histone H3 regulates DOT1L functions including histone H3 'Lys-79' dimethylation (H3K79me2) and gene activation (PubMed:26439302). {ECO:0000269|PubMed:17868029, ECO:0000269|PubMed:26439302}.
Ensembl transtripts involved in fusion geneENST idsENST00000420751, ENST00000354520, 
ENST00000389506, ENST00000534358, 
ENST00000307729, ENST00000377059, 
ENST00000377072, ENST00000446906, 
ENST00000495130, ENST00000377091, 
ENST00000377100, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score79 X 196 X 13=20129217 X 30 X 5=2550
# samples 24130
** MAII scorelog2(241/201292*10)=-6.38411287931608
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(30/2550*10)=-3.08746284125034
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: KMT2A [Title/Abstract] AND MLLT10 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: KMT2A [Title/Abstract] AND MLLT10 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)KMT2A(118355690)-MLLT10(21959376), # samples:3
Anticipated loss of major functional domain due to fusion event.KMT2A-MLLT10 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.
KMT2A-MLLT10 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.
KMT2A-MLLT10 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.
KMT2A-MLLT10 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.
KMT2A-MLLT10 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
KMT2A-MLLT10 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
KMT2A-MLLT10 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
KMT2A-MLLT10 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
KMT2A-MLLT10 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
KMT2A-MLLT10 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
KMT2A-MLLT10 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF.
KMT2A-MLLT10 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
HgeneKMT2A

GO:0044648

histone H3-K4 dimethylation

25561738

HgeneKMT2A

GO:0045944

positive regulation of transcription by RNA polymerase II

20861184

HgeneKMT2A

GO:0051568

histone H3-K4 methylation

19556245

HgeneKMT2A

GO:0065003

protein-containing complex assembly

15199122

HgeneKMT2A

GO:0080182

histone H3-K4 trimethylation

20861184

HgeneKMT2A

GO:0097692

histone H3-K4 monomethylation

25561738|26324722

TgeneMLLT10

GO:0045944

positive regulation of transcription by RNA polymerase II

17868029



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/chr11:118355690/chr10:21959376)
- 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 buttonRetention analysis results 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, are available here.

check buttonFusion gene breakpoints across KMT2A (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 MLLT10 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


Top

Fusion Amino Acid Sequences


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)
ENST00000534358KMT2Achr11118352807+ENST00000446906MLLT10chr1022016784+677040352350801685
ENST00000534358KMT2Achr11118352807+ENST00000377072MLLT10chr1022016784+677540352350801685
ENST00000534358KMT2Achr11118352807+ENST00000307729MLLT10chr1022016784+689940352352511742
ENST00000534358KMT2Achr11118352807+ENST00000377059MLLT10chr1022016784+677040352350801685
ENST00000389506KMT2Achr11118352807+ENST00000446906MLLT10chr1022016784+67474012050571685
ENST00000389506KMT2Achr11118352807+ENST00000377072MLLT10chr1022016784+67524012050571685
ENST00000389506KMT2Achr11118352807+ENST00000307729MLLT10chr1022016784+68764012052281742
ENST00000389506KMT2Achr11118352807+ENST00000377059MLLT10chr1022016784+67474012050571685
ENST00000354520KMT2Achr11118352807+ENST00000446906MLLT10chr1022016784+67474012050571685
ENST00000354520KMT2Achr11118352807+ENST00000377072MLLT10chr1022016784+67524012050571685
ENST00000354520KMT2Achr11118352807+ENST00000307729MLLT10chr1022016784+68764012052281742
ENST00000354520KMT2Achr11118352807+ENST00000377059MLLT10chr1022016784+67474012050571685
ENST00000534358KMT2Achr11118352809ENST00000446906MLLT10chr1022002698+706140352353711782
ENST00000534358KMT2Achr11118352809ENST00000377072MLLT10chr1022002698+706640352353711782
ENST00000534358KMT2Achr11118352809ENST00000307729MLLT10chr1022002698+719040352355421839
ENST00000534358KMT2Achr11118352809ENST00000377059MLLT10chr1022002698+706140352353711782
ENST00000389506KMT2Achr11118352809ENST00000446906MLLT10chr1022002698+70384012053481782
ENST00000389506KMT2Achr11118352809ENST00000377072MLLT10chr1022002698+70434012053481782
ENST00000389506KMT2Achr11118352809ENST00000307729MLLT10chr1022002698+71674012055191839
ENST00000389506KMT2Achr11118352809ENST00000377059MLLT10chr1022002698+70384012053481782
ENST00000354520KMT2Achr11118352809ENST00000446906MLLT10chr1022002698+70384012053481782
ENST00000354520KMT2Achr11118352809ENST00000377072MLLT10chr1022002698+70434012053481782
ENST00000354520KMT2Achr11118352809ENST00000307729MLLT10chr1022002698+71674012055191839
ENST00000354520KMT2Achr11118352809ENST00000377059MLLT10chr1022002698+70384012053481782
ENST00000534358KMT2Achr11118353210ENST00000446906MLLT10chr1021959377+803941092363492108
ENST00000534358KMT2Achr11118353210ENST00000377072MLLT10chr1021959377+809241092363972124
ENST00000534358KMT2Achr11118353210ENST00000307729MLLT10chr1021959377+816841092365202165
ENST00000534358KMT2Achr11118353210ENST00000377059MLLT10chr1021959377+803941092363492108
ENST00000389506KMT2Achr11118353210ENST00000446906MLLT10chr1021959377+80164086063262108
ENST00000389506KMT2Achr11118353210ENST00000377072MLLT10chr1021959377+80694086063742124
ENST00000389506KMT2Achr11118353210ENST00000307729MLLT10chr1021959377+81454086064972165
ENST00000389506KMT2Achr11118353210ENST00000377059MLLT10chr1021959377+80164086063262108
ENST00000354520KMT2Achr11118353210ENST00000446906MLLT10chr1021959377+80164086063262108
ENST00000354520KMT2Achr11118353210ENST00000377072MLLT10chr1021959377+80694086063742124
ENST00000354520KMT2Achr11118353210ENST00000307729MLLT10chr1021959377+81454086064972165
ENST00000354520KMT2Achr11118353210ENST00000377059MLLT10chr1021959377+80164086063262108
ENST00000534358KMT2Achr11118355029+ENST00000446906MLLT10chr1021959376+817142412364812152
ENST00000534358KMT2Achr11118355029+ENST00000377072MLLT10chr1021959376+822442412365292168
ENST00000534358KMT2Achr11118355029+ENST00000307729MLLT10chr1021959376+830042412366522209
ENST00000534358KMT2Achr11118355029+ENST00000377059MLLT10chr1021959376+817142412364812152
ENST00000389506KMT2Achr11118355029+ENST00000446906MLLT10chr1021959376+81484218064582152
ENST00000389506KMT2Achr11118355029+ENST00000377072MLLT10chr1021959376+82014218065062168
ENST00000389506KMT2Achr11118355029+ENST00000307729MLLT10chr1021959376+82774218066292209
ENST00000389506KMT2Achr11118355029+ENST00000377059MLLT10chr1021959376+81484218064582152
ENST00000354520KMT2Achr11118355029+ENST00000446906MLLT10chr1021959376+81484218064582152
ENST00000354520KMT2Achr11118355029+ENST00000377072MLLT10chr1021959376+82014218065062168
ENST00000354520KMT2Achr11118355029+ENST00000307729MLLT10chr1021959376+82774218066292209
ENST00000354520KMT2Achr11118355029+ENST00000377059MLLT10chr1021959376+81484218064582152
ENST00000534358KMT2Achr11118355690+ENST00000446906MLLT10chr1021959376+828543552365952190
ENST00000534358KMT2Achr11118355690+ENST00000377072MLLT10chr1021959376+833843552366432206
ENST00000534358KMT2Achr11118355690+ENST00000307729MLLT10chr1021959376+841443552367662247
ENST00000534358KMT2Achr11118355690+ENST00000377059MLLT10chr1021959376+828543552365952190
ENST00000389506KMT2Achr11118355690+ENST00000446906MLLT10chr1021959376+82624332065722190
ENST00000389506KMT2Achr11118355690+ENST00000377072MLLT10chr1021959376+83154332066202206
ENST00000389506KMT2Achr11118355690+ENST00000307729MLLT10chr1021959376+83914332067432247
ENST00000389506KMT2Achr11118355690+ENST00000377059MLLT10chr1021959376+82624332065722190
ENST00000534358KMT2Achr11118355029+ENST00000446906MLLT10chr1021875216+872642412370362337
ENST00000534358KMT2Achr11118355029+ENST00000377072MLLT10chr1021875216+877942412370842353
ENST00000534358KMT2Achr11118355029+ENST00000307729MLLT10chr1021875216+885542412372072394
ENST00000534358KMT2Achr11118355029+ENST00000377059MLLT10chr1021875216+872642412370362337
ENST00000389506KMT2Achr11118355029+ENST00000446906MLLT10chr1021875216+87034218070132337
ENST00000389506KMT2Achr11118355029+ENST00000377072MLLT10chr1021875216+87564218070612353
ENST00000389506KMT2Achr11118355029+ENST00000307729MLLT10chr1021875216+88324218071842394
ENST00000389506KMT2Achr11118355029+ENST00000377059MLLT10chr1021875216+87034218070132337
ENST00000354520KMT2Achr11118355029+ENST00000446906MLLT10chr1021875216+87034218070132337
ENST00000354520KMT2Achr11118355029+ENST00000377072MLLT10chr1021875216+87564218070612353
ENST00000354520KMT2Achr11118355029+ENST00000307729MLLT10chr1021875216+88324218071842394
ENST00000354520KMT2Achr11118355029+ENST00000377059MLLT10chr1021875216+87034218070132337
ENST00000534358KMT2Achr11118352809+ENST00000446906MLLT10chr1022002698+706140352353711782
ENST00000534358KMT2Achr11118352809+ENST00000377072MLLT10chr1022002698+706640352353711782
ENST00000534358KMT2Achr11118352809+ENST00000307729MLLT10chr1022002698+719040352355421839
ENST00000534358KMT2Achr11118352809+ENST00000377059MLLT10chr1022002698+706140352353711782
ENST00000389506KMT2Achr11118352809+ENST00000446906MLLT10chr1022002698+70384012053481782
ENST00000389506KMT2Achr11118352809+ENST00000377072MLLT10chr1022002698+70434012053481782
ENST00000389506KMT2Achr11118352809+ENST00000307729MLLT10chr1022002698+71674012055191839
ENST00000389506KMT2Achr11118352809+ENST00000377059MLLT10chr1022002698+70384012053481782
ENST00000354520KMT2Achr11118352809+ENST00000446906MLLT10chr1022002698+70384012053481782
ENST00000354520KMT2Achr11118352809+ENST00000377072MLLT10chr1022002698+70434012053481782
ENST00000354520KMT2Achr11118352809+ENST00000307729MLLT10chr1022002698+71674012055191839
ENST00000354520KMT2Achr11118352809+ENST00000377059MLLT10chr1022002698+70384012053481782

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
ENST00000534358ENST00000446906KMT2Achr11118355029+MLLT10chr1021959376+0.0007019010.9992981
ENST00000534358ENST00000377072KMT2Achr11118355029+MLLT10chr1021959376+0.000504390.9994956
ENST00000534358ENST00000307729KMT2Achr11118355029+MLLT10chr1021959376+0.0010865430.9989135
ENST00000534358ENST00000377059KMT2Achr11118355029+MLLT10chr1021959376+0.0007019010.9992981
ENST00000389506ENST00000446906KMT2Achr11118355029+MLLT10chr1021959376+0.0006805380.99931943
ENST00000389506ENST00000377072KMT2Achr11118355029+MLLT10chr1021959376+0.000488630.99951136
ENST00000389506ENST00000307729KMT2Achr11118355029+MLLT10chr1021959376+0.0010540650.998946
ENST00000389506ENST00000377059KMT2Achr11118355029+MLLT10chr1021959376+0.0006805380.99931943
ENST00000354520ENST00000446906KMT2Achr11118355029+MLLT10chr1021959376+0.0006805380.99931943
ENST00000354520ENST00000377072KMT2Achr11118355029+MLLT10chr1021959376+0.000488630.99951136
ENST00000354520ENST00000307729KMT2Achr11118355029+MLLT10chr1021959376+0.0010540650.998946
ENST00000354520ENST00000377059KMT2Achr11118355029+MLLT10chr1021959376+0.0006805380.99931943
ENST00000534358ENST00000446906KMT2Achr11118355690+MLLT10chr1021959376+0.0004096630.99959034
ENST00000534358ENST00000377072KMT2Achr11118355690+MLLT10chr1021959376+0.0007540040.999246
ENST00000534358ENST00000307729KMT2Achr11118355690+MLLT10chr1021959376+0.0007644810.9992355
ENST00000534358ENST00000377059KMT2Achr11118355690+MLLT10chr1021959376+0.0004096630.99959034
ENST00000389506ENST00000446906KMT2Achr11118355690+MLLT10chr1021959376+0.0003965620.99960345
ENST00000389506ENST00000377072KMT2Achr11118355690+MLLT10chr1021959376+0.0007309560.99926907
ENST00000389506ENST00000307729KMT2Achr11118355690+MLLT10chr1021959376+0.0007414720.99925846
ENST00000389506ENST00000377059KMT2Achr11118355690+MLLT10chr1021959376+0.0003965620.99960345
ENST00000534358ENST00000446906KMT2Achr11118355029+MLLT10chr1021875216+0.0003256940.9996743
ENST00000534358ENST00000377072KMT2Achr11118355029+MLLT10chr1021875216+0.0001813630.9998186
ENST00000534358ENST00000307729KMT2Achr11118355029+MLLT10chr1021875216+0.0006156370.9993843
ENST00000534358ENST00000377059KMT2Achr11118355029+MLLT10chr1021875216+0.0003256940.9996743
ENST00000389506ENST00000446906KMT2Achr11118355029+MLLT10chr1021875216+0.0003151130.99968493
ENST00000389506ENST00000377072KMT2Achr11118355029+MLLT10chr1021875216+0.0001747770.9998253
ENST00000389506ENST00000307729KMT2Achr11118355029+MLLT10chr1021875216+0.0005969550.999403
ENST00000389506ENST00000377059KMT2Achr11118355029+MLLT10chr1021875216+0.0003151130.99968493
ENST00000354520ENST00000446906KMT2Achr11118355029+MLLT10chr1021875216+0.0003151130.99968493
ENST00000354520ENST00000377072KMT2Achr11118355029+MLLT10chr1021875216+0.0001747770.9998253
ENST00000354520ENST00000307729KMT2Achr11118355029+MLLT10chr1021875216+0.0005969550.999403
ENST00000354520ENST00000377059KMT2Achr11118355029+MLLT10chr1021875216+0.0003151130.99968493
ENST00000534358ENST00000446906KMT2Achr11118352809+MLLT10chr1022002698+0.0004481510.99955183
ENST00000534358ENST00000377072KMT2Achr11118352809+MLLT10chr1022002698+0.0004419830.99955803
ENST00000534358ENST00000307729KMT2Achr11118352809+MLLT10chr1022002698+0.0005253390.9994747
ENST00000534358ENST00000377059KMT2Achr11118352809+MLLT10chr1022002698+0.0004481510.99955183
ENST00000389506ENST00000446906KMT2Achr11118352809+MLLT10chr1022002698+0.0004330850.99956685
ENST00000389506ENST00000377072KMT2Achr11118352809+MLLT10chr1022002698+0.0004270850.99957293
ENST00000389506ENST00000307729KMT2Achr11118352809+MLLT10chr1022002698+0.0005074770.9994925
ENST00000389506ENST00000377059KMT2Achr11118352809+MLLT10chr1022002698+0.0004330850.99956685
ENST00000354520ENST00000446906KMT2Achr11118352809+MLLT10chr1022002698+0.0004330850.99956685
ENST00000354520ENST00000377072KMT2Achr11118352809+MLLT10chr1022002698+0.0004270850.99957293
ENST00000354520ENST00000307729KMT2Achr11118352809+MLLT10chr1022002698+0.0005074770.9994925
ENST00000354520ENST00000377059KMT2Achr11118352809+MLLT10chr1022002698+0.0004330850.99956685

check button Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones.

Get the fusion protein sequences from here.

Fusion protein sequence information is available in the fasta format.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

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Fusion Protein Breakpoint Sequences for KMT2A-MLLT10

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
KMT2Achr11118352807MLLT10chr10220167844012874RDADKSVEKDKSRERDREREKENKRE
KMT2Achr11118352807MLLT10chr10220167844035874RDADKSVEKDKSRERDREREKENKRE
KMT2Achr11118352809MLLT10chr10220026984012874RDADKSVEKDKSRERDREREKENKRE
KMT2Achr11118352809MLLT10chr10220026984035874RDADKSVEKDKSRERDREREKENKRE
KMT2Achr11118353210MLLT10chr10219593774086873DRDADKSVEKDKSRERDREREKENKR
KMT2Achr11118353210MLLT10chr10219593774109873DRDADKSVEKDKSRERDREREKENKR
KMT2Achr11118355029MLLT10chr10218752164218873DRDADKSVEKDKSRERDREREKENKR
KMT2Achr11118355029MLLT10chr10218752164218874RDADKSVEKDKSRERDREREKENKRE
KMT2Achr11118355029MLLT10chr10218752164241873DRDADKSVEKDKSRERDREREKENKR
KMT2Achr11118355029MLLT10chr10218752164241874RDADKSVEKDKSRERDREREKENKRE
KMT2Achr11118355029MLLT10chr10219593764218874RDADKSVEKDKSRERDREREKENKRE
KMT2Achr11118355029MLLT10chr10219593764241874RDADKSVEKDKSRERDREREKENKRE
KMT2Achr11118355690MLLT10chr10219593764332874RDADKSVEKDKSRERDREREKENKRE
KMT2Achr11118355690MLLT10chr10219593764355874RDADKSVEKDKSRERDREREKENKRE

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Potential FusionNeoAntigen Information of KMT2A-MLLT10 in HLA I

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.

check button Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)
Fusion geneHchrHbpTgeneTchrTbpHLA IFusionNeoAntigen peptideBinding scoreImmunogenic scoreNeoantigen start (at BP 13)Neoantigen end (at BP 13)

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Potential FusionNeoAntigen Information of KMT2A-MLLT10 in HLA II

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.
KMT2A-MLLT10_118352807_22016784.msa

check button Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).
Fusion geneHchrHbpTgeneTchrTbpHLA IIFusionNeoAntigen peptideNeoantigen start (at BP 13)Neoantigen end (at BP 13)
KMT2A-MLLT10chr11118352807chr10220167844012DRB1-0301DKSVEKDKSRERDRE318
KMT2A-MLLT10chr11118352807chr10220167844012DRB1-0303DKSVEKDKSRERDRE318
KMT2A-MLLT10chr11118352807chr10220167844012DRB1-0303ADKSVEKDKSRERDR217
KMT2A-MLLT10chr11118352807chr10220167844012DRB1-0307DKSVEKDKSRERDRE318
KMT2A-MLLT10chr11118352807chr10220167844012DRB1-0313DKSVEKDKSRERDRE318
KMT2A-MLLT10chr11118352807chr10220167844012DRB1-0315DKSVEKDKSRERDRE318
KMT2A-MLLT10chr11118352807chr10220167844012DRB1-0318DKSVEKDKSRERDRE318
KMT2A-MLLT10chr11118352807chr10220167844012DRB1-0320DKSVEKDKSRERDRE318
KMT2A-MLLT10chr11118352807chr10220167844012DRB1-0320ADKSVEKDKSRERDR217
KMT2A-MLLT10chr11118352807chr10220167844012DRB1-0322DKSVEKDKSRERDRE318
KMT2A-MLLT10chr11118352807chr10220167844012DRB1-0326DKSVEKDKSRERDRE318
KMT2A-MLLT10chr11118352807chr10220167844012DRB1-0328DKSVEKDKSRERDRE318
KMT2A-MLLT10chr11118352807chr10220167844012DRB1-0330DKSVEKDKSRERDRE318
KMT2A-MLLT10chr11118352807chr10220167844012DRB1-0332DKSVEKDKSRERDRE318
KMT2A-MLLT10chr11118352807chr10220167844012DRB1-0334DKSVEKDKSRERDRE318
KMT2A-MLLT10chr11118352807chr10220167844012DRB1-0336DKSVEKDKSRERDRE318
KMT2A-MLLT10chr11118352807chr10220167844012DRB1-0342DKSVEKDKSRERDRE318
KMT2A-MLLT10chr11118352807chr10220167844012DRB1-0342ADKSVEKDKSRERDR217
KMT2A-MLLT10chr11118352807chr10220167844012DRB1-0344DKSVEKDKSRERDRE318
KMT2A-MLLT10chr11118352807chr10220167844012DRB1-0346DKSVEKDKSRERDRE318
KMT2A-MLLT10chr11118352807chr10220167844012DRB1-0348DKSVEKDKSRERDRE318
KMT2A-MLLT10chr11118352807chr10220167844012DRB1-0348ADKSVEKDKSRERDR217
KMT2A-MLLT10chr11118352807chr10220167844012DRB1-0350DKSVEKDKSRERDRE318
KMT2A-MLLT10chr11118352807chr10220167844012DRB1-0352DKSVEKDKSRERDRE318
KMT2A-MLLT10chr11118352807chr10220167844012DRB1-0354DKSVEKDKSRERDRE318
KMT2A-MLLT10chr11118352807chr10220167844012DRB1-1107DKSVEKDKSRERDRE318
KMT2A-MLLT10chr11118352807chr10220167844012DRB5-0106DKSVEKDKSRERDRE318
KMT2A-MLLT10chr11118352807chr10220167844012DRB5-0106ADKSVEKDKSRERDR217
KMT2A-MLLT10chr11118352807chr10220167844012DRB5-0111DKSVEKDKSRERDRE318

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Fusion breakpoint peptide structures of KMT2A-MLLT10

check button3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens
* The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA.

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of KMT2A-MLLT10

check buttonVirtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.
HLA allelePDB IDFile nameBPseqDocking scoreGlide score

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Vaccine Design for the FusionNeoAntigens of KMT2A-MLLT10

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptide sequenceFusionNeoAntigen RNA sequence

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
KMT2A-MLLT10chr11118352807chr1022016784217ADKSVEKDKSRERDRCCAAGAAAAAGCAGCCTCCACCACCAGAATCAGATCAAGATCTTG
KMT2A-MLLT10chr11118352807chr1022016784318DKSVEKDKSRERDREAGAAAAAGCAGCCTCCACCACCAGAATCAGATCAAGATCTTGGAG

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Information of the samples that have these potential fusion neoantigens of KMT2A-MLLT10

check button These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.
Cancer typeFusion geneHchrHbpHenstTchrTbpTenstSample

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Potential target of CAR-T therapy development for KMT2A-MLLT10

check button Predicted 3D structure. We used RoseTTAFold.

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, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features


* Minus value of BPloci means that the break point is located before the CDS.
- In-frame and retained 'Transmembrane'.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

check button Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.
HgeneHchrHbpHenstTgeneTchrTbpTenstDeepLoc result

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Related Drugs to KMT2A-MLLT10

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 KMT2A-MLLT10

check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID
KMT2AMLLT10Lung AdenocarcinomaMyCancerGenome
KMT2AMLLT10Acute Myeloid LeukemiaMyCancerGenome
KMT2AMLLT10Bladder Urothelial CarcinomaMyCancerGenome
KMT2AMLLT10Breast Invasive Ductal CarcinomaMyCancerGenome
KMT2AMLLT10Colon AdenocarcinomaMyCancerGenome

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneKMT2AC2826025Mixed phenotype acute leukemia3ORPHANET
HgeneKMT2AC0023418leukemia2CTD_human
HgeneKMT2AC0023452Childhood Acute Lymphoblastic Leukemia2CTD_human
HgeneKMT2AC0023453L2 Acute Lymphoblastic Leukemia2CTD_human
HgeneKMT2AC0023466Leukemia, Monocytic, Chronic2CTD_human
HgeneKMT2AC0023467Leukemia, Myelocytic, Acute2CTD_human
HgeneKMT2AC0023470Myeloid Leukemia2CTD_human
HgeneKMT2AC0026998Acute Myeloid Leukemia, M12CTD_human
HgeneKMT2AC1854630Growth Deficiency and Mental Retardation with Facial Dysmorphism2CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneKMT2AC1879321Acute Myeloid Leukemia (AML-M2)2CTD_human
HgeneKMT2AC1961102Precursor Cell Lymphoblastic Leukemia Lymphoma2CTD_human
HgeneKMT2AC0001418Adenocarcinoma1CTD_human
HgeneKMT2AC0004403Autosome Abnormalities1CTD_human
HgeneKMT2AC0005684Malignant neoplasm of urinary bladder1CTD_human
HgeneKMT2AC0005695Bladder Neoplasm1CTD_human
HgeneKMT2AC0007138Carcinoma, Transitional Cell1CTD_human
HgeneKMT2AC0008625Chromosome Aberrations1CTD_human
HgeneKMT2AC0023448Lymphoid leukemia1CTD_human
HgeneKMT2AC0023465Acute monocytic leukemia1CTD_human
HgeneKMT2AC0023479Acute myelomonocytic leukemia1CTD_human
HgeneKMT2AC0024623Malignant neoplasm of stomach1CTD_human
HgeneKMT2AC0033578Prostatic Neoplasms1CTD_human
HgeneKMT2AC0036341Schizophrenia1PSYGENET
HgeneKMT2AC0038356Stomach Neoplasms1CTD_human
HgeneKMT2AC0149925Small cell carcinoma of lung1CTD_human
HgeneKMT2AC0205641Adenocarcinoma, Basal Cell1CTD_human
HgeneKMT2AC0205642Adenocarcinoma, Oxyphilic1CTD_human
HgeneKMT2AC0205643Carcinoma, Cribriform1CTD_human
HgeneKMT2AC0205644Carcinoma, Granular Cell1CTD_human
HgeneKMT2AC0205645Adenocarcinoma, Tubular1CTD_human
HgeneKMT2AC0270972Cornelia De Lange Syndrome1ORPHANET
HgeneKMT2AC0280141Acute Undifferentiated Leukemia1ORPHANET
HgeneKMT2AC0376358Malignant neoplasm of prostate1CTD_human
HgeneKMT2AC0856823Undifferentiated type acute leukemia1ORPHANET
HgeneKMT2AC1535926Neurodevelopmental Disorders1CTD_human
HgeneKMT2AC1708349Hereditary Diffuse Gastric Cancer1CTD_human
HgeneKMT2AC2239176Liver carcinoma1CTD_human
HgeneKMT2AC2930974Acute erythroleukemia1CTD_human
HgeneKMT2AC2930975Acute erythroleukemia - M6a subtype1CTD_human
HgeneKMT2AC2930976Acute myeloid leukemia FAB-M61CTD_human
HgeneKMT2AC2930977Acute erythroleukemia - M6b subtype1CTD_human
TgeneMLLT10C0007134Renal Cell Carcinoma1CTD_human
TgeneMLLT10C0025202melanoma1CTD_human
TgeneMLLT10C0025286Meningioma1CTD_human
TgeneMLLT10C0205834Meningiomas, Multiple1CTD_human
TgeneMLLT10C0259785Malignant Meningioma1CTD_human
TgeneMLLT10C0279702Conventional (Clear Cell) Renal Cell Carcinoma1CTD_human
TgeneMLLT10C0281784Benign Meningioma1CTD_human
TgeneMLLT10C0334605Meningothelial meningioma1CTD_human
TgeneMLLT10C0334606Fibrous Meningioma1CTD_human
TgeneMLLT10C0334607Psammomatous Meningioma1CTD_human
TgeneMLLT10C0334608Angiomatous Meningioma1CTD_human
TgeneMLLT10C0334609Hemangioblastic Meningioma1CTD_human
TgeneMLLT10C0334610Hemangiopericytic Meningioma1CTD_human
TgeneMLLT10C0334611Transitional Meningioma1CTD_human
TgeneMLLT10C0347515Spinal Meningioma1CTD_human
TgeneMLLT10C0349604Intracranial Meningioma1CTD_human
TgeneMLLT10C0431121Clear Cell Meningioma1CTD_human
TgeneMLLT10C0457190Xanthomatous Meningioma1CTD_human
TgeneMLLT10C0751303Cerebral Convexity Meningioma1CTD_human
TgeneMLLT10C0751304Parasagittal Meningioma1CTD_human
TgeneMLLT10C1266042Chromophobe Renal Cell Carcinoma1CTD_human
TgeneMLLT10C1266043Sarcomatoid Renal Cell Carcinoma1CTD_human
TgeneMLLT10C1266044Collecting Duct Carcinoma of the Kidney1CTD_human
TgeneMLLT10C1306837Papillary Renal Cell Carcinoma1CTD_human
TgeneMLLT10C1334261Intraorbital Meningioma1CTD_human
TgeneMLLT10C1334271Intraventricular Meningioma1CTD_human
TgeneMLLT10C1335107Olfactory Groove Meningioma1CTD_human
TgeneMLLT10C1384406Secretory meningioma1CTD_human
TgeneMLLT10C1384408Microcystic meningioma1CTD_human
TgeneMLLT10C1527197Angioblastic Meningioma1CTD_human
TgeneMLLT10C1565950Posterior Fossa Meningioma1CTD_human
TgeneMLLT10C1565951Sphenoid Wing Meningioma1CTD_human
TgeneMLLT10C1961099Precursor T-Cell Lymphoblastic Leukemia-Lymphoma1ORPHANET
TgeneMLLT10C3163622Papillary Meningioma1CTD_human