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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:KMT2D-HLA-DPA1 (FusionGDB2 ID:43033)

Fusion Gene Summary for KMT2D-HLA-DPA1

check button Fusion gene summary
Fusion gene informationFusion gene name: KMT2D-HLA-DPA1
Fusion gene ID: 43033
HgeneTgene
Gene symbol

KMT2D

HLA-DPA1

Gene ID

8085

3113

Gene namelysine methyltransferase 2Dmajor histocompatibility complex, class II, DP alpha 1
SynonymsAAD10|ALR|CAGL114|KABUK1|KMS|MLL2|MLL4|TNRC21DP(W3)|DP(W4)|DPA1|HLA-DP1A|HLA-DPB1|HLADP|HLASB|PLT1
Cytomap

12q13.12

6p21.32

Type of geneprotein-codingprotein-coding
Descriptionhistone-lysine N-methyltransferase 2DALL1-related proteinKabuki make-up syndromeKabuki mental retardation syndromehistone-lysine N-methyltransferase MLL2lysine (K)-specific methyltransferase 2Dlysine N-methyltransferase 2Dmyeloid/lymphoid or mixed-HLA class II histocompatibility antigen, DP alpha 1 chainHLA DPA1HLA-DPA1*01:03:01:NewHLA-DPA1*02:01:01:NEWHLA-SB alpha chainMHC class II DP alpha chainMHC class II DP3-alphaMHC class II HLA-DPA1 antigen
Modification date2020031620200313
UniProtAcc

O14686

P20036

Ensembl transtripts involved in fusion geneENST00000301067, ENST00000549743, 
ENST00000419277, ENST00000428995, 
ENST00000463066, ENST00000443117, 
ENST00000551196, ENST00000480521, 
ENST00000415247, ENST00000484255, 
ENST00000454805, ENST00000549300, 
ENST00000475500, ENST00000374808, 
ENST00000552158, ENST00000488565, 
ENST00000383224, ENST00000551933, 
ENST00000474244, ENST00000422504, 
ENST00000550806, ENST00000494775, 
ENST00000515317, ENST00000550456, 
ENST00000502285, 
Fusion gene scores* DoF score12 X 12 X 7=10086 X 9 X 1=54
# samples 139
** MAII scorelog2(13/1008*10)=-2.95491211047146
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/54*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: KMT2D [Title/Abstract] AND HLA-DPA1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointKMT2D(49445846)-HLA-DPA1(33036930), # samples:2
Anticipated loss of major functional domain due to fusion event.
* 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
HgeneKMT2D

GO:0043627

response to estrogen

16603732

HgeneKMT2D

GO:0044648

histone H3-K4 dimethylation

26320581

HgeneKMT2D

GO:0080182

histone H3-K4 trimethylation

26320581

HgeneKMT2D

GO:0097692

histone H3-K4 monomethylation

26320581

TgeneHLA-DPA1

GO:0071346

cellular response to interferon-gamma

8568247


check buttonFusion gene breakpoints across KMT2D (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 HLA-DPA1 (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
ChiTaRS5.0N/ABF931318KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
ChiTaRS5.0N/ABF931405KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-


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Fusion Gene ORF analysis for KMT2D-HLA-DPA1

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
intron-3CDSENST00000301067ENST00000419277KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-3CDSENST00000301067ENST00000428995KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000301067ENST00000463066KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000301067ENST00000443117KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000301067ENST00000551196KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000301067ENST00000480521KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000301067ENST00000415247KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000301067ENST00000484255KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000301067ENST00000454805KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000301067ENST00000549300KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000301067ENST00000475500KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000301067ENST00000374808KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000301067ENST00000552158KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000301067ENST00000488565KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000301067ENST00000383224KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000301067ENST00000551933KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000301067ENST00000474244KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000301067ENST00000422504KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000301067ENST00000550806KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000301067ENST00000494775KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000301067ENST00000515317KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000301067ENST00000550456KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000301067ENST00000502285KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-3CDSENST00000549743ENST00000419277KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-3CDSENST00000549743ENST00000428995KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000549743ENST00000463066KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000549743ENST00000443117KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000549743ENST00000551196KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000549743ENST00000480521KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000549743ENST00000415247KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000549743ENST00000484255KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000549743ENST00000454805KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000549743ENST00000549300KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000549743ENST00000475500KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000549743ENST00000374808KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000549743ENST00000552158KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000549743ENST00000488565KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000549743ENST00000383224KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000549743ENST00000551933KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000549743ENST00000474244KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000549743ENST00000422504KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000549743ENST00000550806KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000549743ENST00000494775KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000549743ENST00000515317KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000549743ENST00000550456KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-
intron-intronENST00000549743ENST00000502285KMT2Dchr12

49445846

-HLA-DPA1chr6

33036930

-

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 KMT2D-HLA-DPA1


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 KMT2D-HLA-DPA1


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
KMT2D

O14686

HLA-DPA1

P20036

FUNCTION: Histone methyltransferase. Methylates 'Lys-4' of histone H3 (H3K4me). H3K4me represents a specific tag for epigenetic transcriptional activation. Acts as a coactivator for estrogen receptor by being recruited by ESR1, thereby activating transcription. {ECO:0000269|PubMed:16603732, ECO:0000269|PubMed:17500065, ECO:0000269|PubMed:17851529}.FUNCTION: Binds peptides derived from antigens that access the endocytic route of antigen presenting cells (APC) and presents them on the cell surface for recognition by the CD4 T-cells. The peptide binding cleft accommodates peptides of 10-30 residues. The peptides presented by MHC class II molecules are generated mostly by degradation of proteins that access the endocytic route, where they are processed by lysosomal proteases and other hydrolases. Exogenous antigens that have been endocytosed by the APC are thus readily available for presentation via MHC II molecules, and for this reason this antigen presentation pathway is usually referred to as exogenous. As membrane proteins on their way to degradation in lysosomes as part of their normal turn-over are also contained in the endosomal/lysosomal compartments, exogenous antigens must compete with those derived from endogenous components. Autophagy is also a source of endogenous peptides, autophagosomes constitutively fuse with MHC class II loading compartments. In addition to APCs, other cells of the gastrointestinal tract, such as epithelial cells, express MHC class II molecules and CD74 and act as APCs, which is an unusual trait of the GI tract. To produce a MHC class II molecule that presents an antigen, three MHC class II molecules (heterodimers of an alpha and a beta chain) associate with a CD74 trimer in the ER to form a heterononamer. Soon after the entry of this complex into the endosomal/lysosomal system where antigen processing occurs, CD74 undergoes a sequential degradation by various proteases, including CTSS and CTSL, leaving a small fragment termed CLIP (class-II-associated invariant chain peptide). The removal of CLIP is facilitated by HLA-DM via direct binding to the alpha-beta-CLIP complex so that CLIP is released. HLA-DM stabilizes MHC class II molecules until primary high affinity antigenic peptides are bound. The MHC II molecule bound to a peptide is then transported to the cell membrane surface. In B-cells, the interaction between HLA-DM and MHC class II molecules is regulated by HLA-DO. Primary dendritic cells (DCs) also to express HLA-DO. Lysosomal microenvironment has been implicated in the regulation of antigen loading into MHC II molecules, increased acidification produces increased proteolysis and efficient peptide loading.

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 KMT2D-HLA-DPA1


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 KMT2D-HLA-DPA1


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 KMT2D-HLA-DPA1


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 KMT2D-HLA-DPA1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneKMT2DC0796004Kabuki make-up syndrome18CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneKMT2DC0005684Malignant neoplasm of urinary bladder1CTD_human
HgeneKMT2DC0005695Bladder Neoplasm1CTD_human
HgeneKMT2DC0006142Malignant neoplasm of breast1CTD_human
HgeneKMT2DC0010701Phyllodes Tumor1CTD_human
HgeneKMT2DC0021364Male infertility1CTD_human
HgeneKMT2DC0024301Lymphoma, Follicular1CTD_human
HgeneKMT2DC0026010Microphthalmos1GENOMICS_ENGLAND
HgeneKMT2DC0033578Prostatic Neoplasms1CTD_human
HgeneKMT2DC0036920Sezary Syndrome1CTD_human
HgeneKMT2DC0079744Diffuse Large B-Cell Lymphoma1CTD_human
HgeneKMT2DC0079745Lymphoma, Large-Cell, Follicular1CTD_human
HgeneKMT2DC0079758Lymphoma, Mixed-Cell, Follicular1CTD_human
HgeneKMT2DC0079765Lymphoma, Small Cleaved-Cell, Follicular1CTD_human
HgeneKMT2DC0079772T-Cell Lymphoma1CTD_human
HgeneKMT2DC0152423Congenital small ears1GENOMICS_ENGLAND
HgeneKMT2DC0279626Squamous cell carcinoma of esophagus1CTD_human
HgeneKMT2DC0376358Malignant neoplasm of prostate1CTD_human
HgeneKMT2DC0600066Malignant Cystosarcoma Phyllodes1CTD_human
HgeneKMT2DC0678222Breast Carcinoma1CTD_human
HgeneKMT2DC0848676Subfertility, Male1CTD_human
HgeneKMT2DC0917731Male sterility1CTD_human
HgeneKMT2DC1257931Mammary Neoplasms, Human1CTD_human
HgeneKMT2DC1458155Mammary Neoplasms1CTD_human
HgeneKMT2DC1708353Hereditary Paraganglioma-Pheochromocytoma Syndrome1CLINGEN
HgeneKMT2DC1956130Lymphoma, Follicular, Grade 11CTD_human
HgeneKMT2DC1956131Lymphoma, Follicular, Grade 31CTD_human
HgeneKMT2DC1956132Lymphoma, Follicular, Grade 21CTD_human
HgeneKMT2DC4704874Mammary Carcinoma, Human1CTD_human
TgeneHLA-DPA1C0162823Dermatitis, Irritant1CTD_human
TgeneHLA-DPA1C0524909Hepatitis B, Chronic1CTD_human
TgeneHLA-DPA1C3495801Granulomatosis with polyangiitis1ORPHANET