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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:NEBL-KMT2A

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: NEBL-KMT2A
FusionPDB ID: 58344
FusionGDB2.0 ID: 58344
HgeneTgene
Gene symbol

NEBL

KMT2A

Gene ID

10529

4297

Gene namenebulettelysine methyltransferase 2A
SynonymsC10orf113|LASP2|LNEBL|bA165O3.1ALL-1|CXXC7|HRX|HTRX1|MLL|MLL1|MLL1A|TRX1|WDSTS
Cytomap

10p12.31

11q23.3

Type of geneprotein-codingprotein-coding
DescriptionnebuletteLIM and SH3 protein 2LIM-nebuletteactin-binding Z-disk proteinhistone-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 date2020031320200319
UniProtAcc

O76041

Main function of 5'-partner protein: FUNCTION: Binds to actin and plays an important role in the assembly of the Z-disk. May functionally link sarcomeric actin to the desmin intermediate filaments in the heart muscle sarcomeres (PubMed:27733623). Isoform 2 might play a role in the assembly of focal adhesion (PubMed:15004028). {ECO:0000269|PubMed:15004028, ECO:0000269|PubMed:27733623}.

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}.
Ensembl transtripts involved in fusion geneENST idsENST00000377159, ENST00000417816, 
ENST00000377119, ENST00000377122, 
ENST00000464278, 
ENST00000420751, 
ENST00000354520, ENST00000389506, 
ENST00000534358, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score15 X 12 X 6=108031 X 72 X 3=6696
# samples 1679
** MAII scorelog2(16/1080*10)=-2.75488750216347
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
Fusion gene context

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

Fusion neoantigen context

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

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)KMT2A(118353224)-NEBL(21250710), # samples:1
NEBL(21309045)-KMT2A(118354896), # samples:1
Anticipated loss of major functional domain due to fusion event.NEBL-KMT2A 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.
NEBL-KMT2A 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.
NEBL-KMT2A 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.
NEBL-KMT2A 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
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 button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr10:118353224/chr11:21250710)
- 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 NEBL (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 KMT2A (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 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)
ENST00000417816NEBLchr1021309045-ENST00000534358KMT2Achr11118354896+1308860335484352693
ENST00000417816NEBLchr1021309045-ENST00000389506KMT2Achr11118354896+1017260335484262690
ENST00000417816NEBLchr1021309045-ENST00000354520KMT2Achr11118354896+1083760335483122652
ENST00000377159NEBLchr1021309045-ENST00000534358KMT2Achr11118354896+12634149279812659
ENST00000377159NEBLchr1021309045-ENST00000389506KMT2Achr11118354896+9718149279722656
ENST00000377159NEBLchr1021309045-ENST00000354520KMT2Achr11118354896+10383149278582618

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
ENST00000417816ENST00000534358NEBLchr1021309045-KMT2Achr11118354896+0.0003687090.9996313
ENST00000417816ENST00000389506NEBLchr1021309045-KMT2Achr11118354896+0.0006558850.99934405
ENST00000417816ENST00000354520NEBLchr1021309045-KMT2Achr11118354896+0.0007607570.9992392
ENST00000377159ENST00000534358NEBLchr1021309045-KMT2Achr11118354896+0.0002369560.9997631
ENST00000377159ENST00000389506NEBLchr1021309045-KMT2Achr11118354896+0.0004221220.9995778
ENST00000377159ENST00000354520NEBLchr1021309045-KMT2Achr11118354896+0.0004856390.99951434

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 NEBL-KMT2A

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
NEBLchr1021309045KMT2Achr1111835489614949NLRLKQQSELQSQEKPPPVNKQENAG
NEBLchr1021309045KMT2Achr1111835489660383NLRLKQQSELQSQEKPPPVNKQENAG

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Potential FusionNeoAntigen Information of NEBL-KMT2A 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.
NEBL-KMT2A_21309045_118354896.msa

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)
NEBL-KMT2Achr1021309045chr11118354896149HLA-B45:01SELQSQEKP0.99530.9556716
NEBL-KMT2Achr1021309045chr11118354896149HLA-B50:02SELQSQEKP0.99170.7423716
NEBL-KMT2Achr1021309045chr11118354896149HLA-B47:01QEKPPPVNK0.76060.5451221
NEBL-KMT2Achr1021309045chr11118354896149HLA-B41:01SELQSQEKP0.74030.9527716
NEBL-KMT2Achr1021309045chr11118354896149HLA-B50:01SELQSQEKP0.65770.7989716
NEBL-KMT2Achr1021309045chr11118354896149HLA-B45:01SELQSQEKPP0.98970.9759717
NEBL-KMT2Achr1021309045chr11118354896149HLA-A30:08SQEKPPPVNK0.87440.67211121
NEBL-KMT2Achr1021309045chr11118354896149HLA-A30:08QSQEKPPPVNK0.99580.67611021
NEBL-KMT2Achr1021309045chr11118354896149HLA-B40:06SELQSQEKP0.99240.7075716
NEBL-KMT2Achr1021309045chr11118354896149HLA-B50:04SELQSQEKP0.65770.7989716
NEBL-KMT2Achr1021309045chr11118354896149HLA-B50:05SELQSQEKP0.65770.7989716
NEBL-KMT2Achr1021309045chr11118354896149HLA-A30:01SQEKPPPVNK0.87150.77051121
NEBL-KMT2Achr1021309045chr11118354896149HLA-A30:01QSQEKPPPVNK0.99530.8311021

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Potential FusionNeoAntigen Information of NEBL-KMT2A 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.

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)

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Fusion breakpoint peptide structures of NEBL-KMT2A

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.
File nameBPseqHgeneTgeneHchrHbpTchrTbpAAlen
7577QSELQSQEKPPPVNNEBLKMT2Achr1021309045chr11118354896149

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

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
HLA-B14:023BVN7577QSELQSQEKPPPVN-7.9962-8.1096
HLA-B14:023BVN7577QSELQSQEKPPPVN-5.70842-6.74372
HLA-B52:013W397577QSELQSQEKPPPVN-6.83737-6.95077
HLA-B52:013W397577QSELQSQEKPPPVN-4.4836-5.5189
HLA-A11:014UQ27577QSELQSQEKPPPVN-10.0067-10.1201
HLA-A11:014UQ27577QSELQSQEKPPPVN-9.03915-10.0745
HLA-A24:025HGA7577QSELQSQEKPPPVN-6.56204-6.67544
HLA-A24:025HGA7577QSELQSQEKPPPVN-5.42271-6.45801
HLA-B44:053DX87577QSELQSQEKPPPVN-7.85648-8.89178
HLA-B44:053DX87577QSELQSQEKPPPVN-5.3978-5.5112
HLA-A02:016TDR7577QSELQSQEKPPPVN-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of NEBL-KMT2A

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
NEBL-KMT2Achr1021309045chr111183548961021QSQEKPPPVNKCAGAGTCAGGAAAAACCACCTCCGGTCAATAAG
NEBL-KMT2Achr1021309045chr111183548961121SQEKPPPVNKAGTCAGGAAAAACCACCTCCGGTCAATAAG
NEBL-KMT2Achr1021309045chr111183548961221QEKPPPVNKCAGGAAAAACCACCTCCGGTCAATAAG
NEBL-KMT2Achr1021309045chr11118354896716SELQSQEKPAGTGAATTGCAGAGTCAGGAAAAACCA
NEBL-KMT2Achr1021309045chr11118354896717SELQSQEKPPAGTGAATTGCAGAGTCAGGAAAAACCACCT

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

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

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
N/ANEBL-KMT2Achr1021309045ENST00000377159chr11118354896ENST00000354520MH319862

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

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 NEBL-KMT2A

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 NEBL-KMT2A

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
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