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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:MLLT4-KMT2A (FusionGDB2 ID:53988)

Fusion Gene Summary for MLLT4-KMT2A

check button Fusion gene summary
Fusion gene informationFusion gene name: MLLT4-KMT2A
Fusion gene ID: 53988
HgeneTgene
Gene symbol

MLLT4

KMT2A

Gene ID

4301

4297

Gene nameafadin, adherens junction formation factorlysine methyltransferase 2A
SynonymsAF6|MLL-AF6|MLLT4|l-afadinALL-1|CXXC7|HRX|HTRX1|MLL|MLL1|MLL1A|TRX1|WDSTS
Cytomap

6q27

11q23.3

Type of geneprotein-codingprotein-coding
DescriptionafadinALL1-fused gene from chromosome 6 proteinmyeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4myeloid/lymphoid or mixed-lineage leukemia; translocated to, 4protein AF-6histone-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-like
Modification date2020032220200319
UniProtAcc.

Q03164

Ensembl transtripts involved in fusion geneENST00000344191, ENST00000351017, 
ENST00000392108, ENST00000392112, 
ENST00000366806, ENST00000447894, 
ENST00000400822, ENST00000507679, 
ENST00000534358, ENST00000389506, 
ENST00000354520, ENST00000420751, 
Fusion gene scores* DoF score15 X 7 X 10=105031 X 72 X 3=6696
# samples 1679
** MAII scorelog2(16/1050*10)=-2.71424551766612
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(79/6696*10)=-3.08337496948588
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MLLT4 [Title/Abstract] AND KMT2A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointKMT2A(118355029)-MLLT4(168265231), # samples:2
MLLT4(168227917)-KMT2A(118352430), # samples:1
Anticipated loss of major functional domain due to fusion event.MLLT4-KMT2A seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF.
MLLT4-KMT2A seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
MLLT4-KMT2A seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
MLLT4-KMT2A seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
MLLT4-KMT2A seems lost the major protein functional domain in Tgene partner, which is a epigenetic 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
TgeneKMT2A

GO:0044648

histone H3-K4 dimethylation

25561738

TgeneKMT2A

GO:0045944

positive regulation of transcription by RNA polymerase II

20861184

TgeneKMT2A

GO:0051568

histone H3-K4 methylation

19556245

TgeneKMT2A

GO:0065003

protein-containing complex assembly

15199122

TgeneKMT2A

GO:0080182

histone H3-K4 trimethylation

20861184

TgeneKMT2A

GO:0097692

histone H3-K4 monomethylation

25561738|26324722


check buttonFusion gene breakpoints across MLLT4 (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 KMT2A (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
ChimerDB4LAMLTCGA-AB-2893_6165JAAXX_3MLLT4chr6

168227917

+KMT2Achr11

118352430

+


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Fusion Gene ORF analysis for MLLT4-KMT2A

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-shiftENST00000344191ENST00000534358MLLT4chr6

168227917

+KMT2Achr11

118352430

+
Frame-shiftENST00000344191ENST00000389506MLLT4chr6

168227917

+KMT2Achr11

118352430

+
Frame-shiftENST00000344191ENST00000354520MLLT4chr6

168227917

+KMT2Achr11

118352430

+
5CDS-intronENST00000344191ENST00000420751MLLT4chr6

168227917

+KMT2Achr11

118352430

+
Frame-shiftENST00000351017ENST00000534358MLLT4chr6

168227917

+KMT2Achr11

118352430

+
Frame-shiftENST00000351017ENST00000389506MLLT4chr6

168227917

+KMT2Achr11

118352430

+
Frame-shiftENST00000351017ENST00000354520MLLT4chr6

168227917

+KMT2Achr11

118352430

+
5CDS-intronENST00000351017ENST00000420751MLLT4chr6

168227917

+KMT2Achr11

118352430

+
Frame-shiftENST00000392108ENST00000534358MLLT4chr6

168227917

+KMT2Achr11

118352430

+
Frame-shiftENST00000392108ENST00000389506MLLT4chr6

168227917

+KMT2Achr11

118352430

+
Frame-shiftENST00000392108ENST00000354520MLLT4chr6

168227917

+KMT2Achr11

118352430

+
5CDS-intronENST00000392108ENST00000420751MLLT4chr6

168227917

+KMT2Achr11

118352430

+
Frame-shiftENST00000392112ENST00000534358MLLT4chr6

168227917

+KMT2Achr11

118352430

+
Frame-shiftENST00000392112ENST00000389506MLLT4chr6

168227917

+KMT2Achr11

118352430

+
Frame-shiftENST00000392112ENST00000354520MLLT4chr6

168227917

+KMT2Achr11

118352430

+
5CDS-intronENST00000392112ENST00000420751MLLT4chr6

168227917

+KMT2Achr11

118352430

+
Frame-shiftENST00000366806ENST00000534358MLLT4chr6

168227917

+KMT2Achr11

118352430

+
Frame-shiftENST00000366806ENST00000389506MLLT4chr6

168227917

+KMT2Achr11

118352430

+
Frame-shiftENST00000366806ENST00000354520MLLT4chr6

168227917

+KMT2Achr11

118352430

+
5CDS-intronENST00000366806ENST00000420751MLLT4chr6

168227917

+KMT2Achr11

118352430

+
Frame-shiftENST00000447894ENST00000534358MLLT4chr6

168227917

+KMT2Achr11

118352430

+
Frame-shiftENST00000447894ENST00000389506MLLT4chr6

168227917

+KMT2Achr11

118352430

+
Frame-shiftENST00000447894ENST00000354520MLLT4chr6

168227917

+KMT2Achr11

118352430

+
5CDS-intronENST00000447894ENST00000420751MLLT4chr6

168227917

+KMT2Achr11

118352430

+
Frame-shiftENST00000400822ENST00000534358MLLT4chr6

168227917

+KMT2Achr11

118352430

+
Frame-shiftENST00000400822ENST00000389506MLLT4chr6

168227917

+KMT2Achr11

118352430

+
Frame-shiftENST00000400822ENST00000354520MLLT4chr6

168227917

+KMT2Achr11

118352430

+
5CDS-intronENST00000400822ENST00000420751MLLT4chr6

168227917

+KMT2Achr11

118352430

+
intron-3CDSENST00000507679ENST00000534358MLLT4chr6

168227917

+KMT2Achr11

118352430

+
intron-3CDSENST00000507679ENST00000389506MLLT4chr6

168227917

+KMT2Achr11

118352430

+
intron-3CDSENST00000507679ENST00000354520MLLT4chr6

168227917

+KMT2Achr11

118352430

+
intron-intronENST00000507679ENST00000420751MLLT4chr6

168227917

+KMT2Achr11

118352430

+

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 MLLT4-KMT2A


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 MLLT4-KMT2A


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
.KMT2A

Q03164

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.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}.

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 MLLT4-KMT2A


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 MLLT4-KMT2A


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 MLLT4-KMT2A


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 MLLT4-KMT2A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneKMT2AC2826025Mixed phenotype acute leukemia3ORPHANET
TgeneKMT2AC0023418leukemia2CTD_human
TgeneKMT2AC0023452Childhood Acute Lymphoblastic Leukemia2CTD_human
TgeneKMT2AC0023453L2 Acute Lymphoblastic Leukemia2CTD_human
TgeneKMT2AC0023466Leukemia, Monocytic, Chronic2CTD_human
TgeneKMT2AC0023467Leukemia, Myelocytic, Acute2CTD_human
TgeneKMT2AC0023470Myeloid Leukemia2CTD_human
TgeneKMT2AC0026998Acute Myeloid Leukemia, M12CTD_human
TgeneKMT2AC1854630Growth Deficiency and Mental Retardation with Facial Dysmorphism2CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneKMT2AC1879321Acute Myeloid Leukemia (AML-M2)2CTD_human
TgeneKMT2AC1961102Precursor Cell Lymphoblastic Leukemia Lymphoma2CTD_human
TgeneKMT2AC0001418Adenocarcinoma1CTD_human
TgeneKMT2AC0004403Autosome Abnormalities1CTD_human
TgeneKMT2AC0005684Malignant neoplasm of urinary bladder1CTD_human
TgeneKMT2AC0005695Bladder Neoplasm1CTD_human
TgeneKMT2AC0007138Carcinoma, Transitional Cell1CTD_human
TgeneKMT2AC0008625Chromosome Aberrations1CTD_human
TgeneKMT2AC0023448Lymphoid leukemia1CTD_human
TgeneKMT2AC0023465Acute monocytic leukemia1CTD_human
TgeneKMT2AC0023479Acute myelomonocytic leukemia1CTD_human
TgeneKMT2AC0024623Malignant neoplasm of stomach1CTD_human
TgeneKMT2AC0033578Prostatic Neoplasms1CTD_human
TgeneKMT2AC0036341Schizophrenia1PSYGENET
TgeneKMT2AC0038356Stomach Neoplasms1CTD_human
TgeneKMT2AC0149925Small cell carcinoma of lung1CTD_human
TgeneKMT2AC0205641Adenocarcinoma, Basal Cell1CTD_human
TgeneKMT2AC0205642Adenocarcinoma, Oxyphilic1CTD_human
TgeneKMT2AC0205643Carcinoma, Cribriform1CTD_human
TgeneKMT2AC0205644Carcinoma, Granular Cell1CTD_human
TgeneKMT2AC0205645Adenocarcinoma, Tubular1CTD_human
TgeneKMT2AC0270972Cornelia De Lange Syndrome1ORPHANET
TgeneKMT2AC0280141Acute Undifferentiated Leukemia1ORPHANET
TgeneKMT2AC0376358Malignant neoplasm of prostate1CTD_human
TgeneKMT2AC0856823Undifferentiated type acute leukemia1ORPHANET
TgeneKMT2AC1535926Neurodevelopmental Disorders1CTD_human
TgeneKMT2AC1708349Hereditary Diffuse Gastric Cancer1CTD_human
TgeneKMT2AC2239176Liver carcinoma1CTD_human
TgeneKMT2AC2930974Acute erythroleukemia1CTD_human
TgeneKMT2AC2930975Acute erythroleukemia - M6a subtype1CTD_human
TgeneKMT2AC2930976Acute myeloid leukemia FAB-M61CTD_human
TgeneKMT2AC2930977Acute erythroleukemia - M6b subtype1CTD_human