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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:MLLT10-DNAJC1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: MLLT10-DNAJC1
FusionPDB ID: 54258
FusionGDB2.0 ID: 54258
HgeneTgene
Gene symbol

MLLT10

DNAJC1

Gene ID

8028

64215

Gene nameMLLT10 histone lysine methyltransferase DOT1L cofactorDnaJ heat shock protein family (Hsp40) member C1
SynonymsAF10DNAJL1|ERdj1|HTJ1|MTJ1
Cytomap

10p12.31

10p12.31

Type of geneprotein-codingprotein-coding
Descriptionprotein 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 protdnaJ homolog subfamily C member 1DnaJ (Hsp40) homolog, subfamily C, member 1DnaJ-like proteindnaJ protein homolog MTJ1
Modification date2020031320200313
UniProtAcc

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}.

Q96DA6

Main function of 5'-partner protein: FUNCTION: Mitochondrial co-chaperone which forms a complex with prohibitins to regulate cardiolipin remodeling (By similarity). May be a component of the PAM complex, a complex required for the translocation of transit peptide-containing proteins from the inner membrane into the mitochondrial matrix in an ATP-dependent manner. May act as a co-chaperone that stimulate the ATP-dependent activity (By similarity). {ECO:0000250|UniProtKB:Q07914, ECO:0000250|UniProtKB:Q9CQV7}.
Ensembl transtripts involved in fusion geneENST idsENST00000307729, ENST00000377059, 
ENST00000377072, ENST00000446906, 
ENST00000377091, ENST00000377100, 
ENST00000495130, 
ENST00000376946, 
ENST00000483085, ENST00000376980, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score18 X 15 X 10=270012 X 9 X 6=648
# samples 2413
** MAII scorelog2(24/2700*10)=-3.49185309632968
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(13/648*10)=-2.31748218985617
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: MLLT10 [Title/Abstract] AND DNAJC1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: MLLT10 [Title/Abstract] AND DNAJC1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)DNAJC1(22094909)-MLLT10(22002701), # samples:1
MLLT10(22002879)-DNAJC1(22193541), # samples:1
Anticipated loss of major functional domain due to fusion event.MLLT10-DNAJC1 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.
MLLT10-DNAJC1 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.
MLLT10-DNAJC1 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.
MLLT10-DNAJC1 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.
DNAJC1-MLLT10 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
DNAJC1-MLLT10 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
DNAJC1-MLLT10 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF.
DNAJC1-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
HgeneMLLT10

GO:0045944

positive regulation of transcription by RNA polymerase II

17868029

TgeneDNAJC1

GO:0050708

regulation of protein secretion

14668352



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/chr10:22094909/chr10:22002701)
- 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 MLLT10 (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 DNAJC1 (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)
ENST00000446906MLLT10chr1022002879+ENST00000376980DNAJC1chr1022193541-331222263303161943
ENST00000377072MLLT10chr1022002879+ENST00000376980DNAJC1chr1022193541-336022743303209959
ENST00000307729MLLT10chr1022002879+ENST00000376980DNAJC1chr1022193541-314220561602991943
ENST00000377059MLLT10chr1022002879+ENST00000376980DNAJC1chr1022193541-2964187802813937

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
ENST00000446906ENST00000376980MLLT10chr1022002879+DNAJC1chr1022193541-0.0015352820.9984647
ENST00000377072ENST00000376980MLLT10chr1022002879+DNAJC1chr1022193541-0.0011947090.9988053
ENST00000307729ENST00000376980MLLT10chr1022002879+DNAJC1chr1022193541-0.0016274480.9983726
ENST00000377059ENST00000376980MLLT10chr1022002879+DNAJC1chr1022193541-0.001656330.9983437

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 MLLT10-DNAJC1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
MLLT10chr1022002879DNAJC1chr10221935411878626AVSSAAPAVATTQDAGQFYAKYKETR
MLLT10chr1022002879DNAJC1chr10221935412056632AVSSAAPAVATTQDAGQFYAKYKETR
MLLT10chr1022002879DNAJC1chr10221935412226632AVSSAAPAVATTQDAGQFYAKYKETR
MLLT10chr1022002879DNAJC1chr10221935412274648AVSSAAPAVATTQDAGQFYAKYKETR

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Potential FusionNeoAntigen Information of MLLT10-DNAJC1 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.
MLLT10-DNAJC1_22002879_22193541.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)
MLLT10-DNAJC1chr1022002879chr10221935412056HLA-B35:08TTQDAGQFY0.9460.91221019
MLLT10-DNAJC1chr1022002879chr10221935412056HLA-B15:17TTQDAGQFY0.92190.90341019
MLLT10-DNAJC1chr1022002879chr10221935412056HLA-B15:17ATTQDAGQF0.90650.8867918
MLLT10-DNAJC1chr1022002879chr10221935412056HLA-B15:02TTQDAGQFY0.89770.92371019
MLLT10-DNAJC1chr1022002879chr10221935412056HLA-B56:01APAVATTQDA0.79990.6269515
MLLT10-DNAJC1chr1022002879chr10221935412056HLA-B15:31TTQDAGQFY0.88250.90161019
MLLT10-DNAJC1chr1022002879chr10221935412056HLA-C15:04TTQDAGQFY0.47210.79761019
MLLT10-DNAJC1chr1022002879chr10221935412056HLA-C03:14TTQDAGQFY0.04580.95171019
MLLT10-DNAJC1chr1022002879chr10221935412056HLA-B35:20TTQDAGQFY0.87660.95691019
MLLT10-DNAJC1chr1022002879chr10221935412056HLA-B57:02ATTQDAGQF0.75310.9431918
MLLT10-DNAJC1chr1022002879chr10221935412056HLA-B15:11TTQDAGQFY0.74690.84391019
MLLT10-DNAJC1chr1022002879chr10221935412056HLA-B15:08TTQDAGQFY0.740.84861019
MLLT10-DNAJC1chr1022002879chr10221935412056HLA-A25:01TTQDAGQFY0.60610.8411019
MLLT10-DNAJC1chr1022002879chr10221935412056HLA-C15:09TTQDAGQFY0.47210.79761019
MLLT10-DNAJC1chr1022002879chr10221935412056HLA-C03:02TTQDAGQFY0.35040.95481019
MLLT10-DNAJC1chr1022002879chr10221935412056HLA-C12:02TTQDAGQFY0.14310.95381019
MLLT10-DNAJC1chr1022002879chr10221935412056HLA-C16:02TTQDAGQFY0.05020.991019
MLLT10-DNAJC1chr1022002879chr10221935412056HLA-C16:01TTQDAGQFY0.01510.97581019
MLLT10-DNAJC1chr1022002879chr10221935412056HLA-C02:02TTQDAGQFY0.00480.96641019
MLLT10-DNAJC1chr1022002879chr10221935412056HLA-C02:10TTQDAGQFY0.00480.96641019
MLLT10-DNAJC1chr1022002879chr10221935412056HLA-B55:02APAVATTQDA0.87890.618515
MLLT10-DNAJC1chr1022002879chr10221935412056HLA-B35:28TQDAGQFYAKY0.99070.91251122

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Potential FusionNeoAntigen Information of MLLT10-DNAJC1 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 MLLT10-DNAJC1

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
6517PAVATTQDAGQFYAMLLT10DNAJC1chr1022002879chr10221935412056

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of MLLT10-DNAJC1

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-B14:023BVN6517PAVATTQDAGQFYA-7.4838-7.5956
HLA-B14:023BVN6517PAVATTQDAGQFYA-3.16066-4.20376
HLA-B52:013W396517PAVATTQDAGQFYA-6.93679-7.04859
HLA-B52:013W396517PAVATTQDAGQFYA-6.10064-7.14374
HLA-A11:014UQ26517PAVATTQDAGQFYA-7.21307-7.32487
HLA-A24:025HGA6517PAVATTQDAGQFYA-6.56769-6.67949
HLA-A24:025HGA6517PAVATTQDAGQFYA-4.65311-5.69621
HLA-B44:053DX86517PAVATTQDAGQFYA-6.68002-6.79182
HLA-B44:053DX86517PAVATTQDAGQFYA-3.22493-4.26803

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Vaccine Design for the FusionNeoAntigens of MLLT10-DNAJC1

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
MLLT10-DNAJC1chr1022002879chr10221935411019TTQDAGQFYACAACTCAGGATGCTGGGCAGTTTTAT
MLLT10-DNAJC1chr1022002879chr10221935411122TQDAGQFYAKYACTCAGGATGCTGGGCAGTTTTATGCTAAATAT
MLLT10-DNAJC1chr1022002879chr1022193541515APAVATTQDAGCCCCTGCTGTTGCTACAACTCAGGATGCT
MLLT10-DNAJC1chr1022002879chr1022193541918ATTQDAGQFGCTACAACTCAGGATGCTGGGCAGTTT

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 MLLT10-DNAJC1

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
READMLLT10-DNAJC1chr1022002879ENST00000307729chr1022193541ENST00000376980TCGA-AG-A020

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Potential target of CAR-T therapy development for MLLT10-DNAJC1

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 MLLT10-DNAJC1

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 MLLT10-DNAJC1

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
HgeneMLLT10C0007134Renal Cell Carcinoma1CTD_human
HgeneMLLT10C0025202melanoma1CTD_human
HgeneMLLT10C0025286Meningioma1CTD_human
HgeneMLLT10C0205834Meningiomas, Multiple1CTD_human
HgeneMLLT10C0259785Malignant Meningioma1CTD_human
HgeneMLLT10C0279702Conventional (Clear Cell) Renal Cell Carcinoma1CTD_human
HgeneMLLT10C0281784Benign Meningioma1CTD_human
HgeneMLLT10C0334605Meningothelial meningioma1CTD_human
HgeneMLLT10C0334606Fibrous Meningioma1CTD_human
HgeneMLLT10C0334607Psammomatous Meningioma1CTD_human
HgeneMLLT10C0334608Angiomatous Meningioma1CTD_human
HgeneMLLT10C0334609Hemangioblastic Meningioma1CTD_human
HgeneMLLT10C0334610Hemangiopericytic Meningioma1CTD_human
HgeneMLLT10C0334611Transitional Meningioma1CTD_human
HgeneMLLT10C0347515Spinal Meningioma1CTD_human
HgeneMLLT10C0349604Intracranial Meningioma1CTD_human
HgeneMLLT10C0431121Clear Cell Meningioma1CTD_human
HgeneMLLT10C0457190Xanthomatous Meningioma1CTD_human
HgeneMLLT10C0751303Cerebral Convexity Meningioma1CTD_human
HgeneMLLT10C0751304Parasagittal Meningioma1CTD_human
HgeneMLLT10C1266042Chromophobe Renal Cell Carcinoma1CTD_human
HgeneMLLT10C1266043Sarcomatoid Renal Cell Carcinoma1CTD_human
HgeneMLLT10C1266044Collecting Duct Carcinoma of the Kidney1CTD_human
HgeneMLLT10C1306837Papillary Renal Cell Carcinoma1CTD_human
HgeneMLLT10C1334261Intraorbital Meningioma1CTD_human
HgeneMLLT10C1334271Intraventricular Meningioma1CTD_human
HgeneMLLT10C1335107Olfactory Groove Meningioma1CTD_human
HgeneMLLT10C1384406Secretory meningioma1CTD_human
HgeneMLLT10C1384408Microcystic meningioma1CTD_human
HgeneMLLT10C1527197Angioblastic Meningioma1CTD_human
HgeneMLLT10C1565950Posterior Fossa Meningioma1CTD_human
HgeneMLLT10C1565951Sphenoid Wing Meningioma1CTD_human
HgeneMLLT10C1961099Precursor T-Cell Lymphoblastic Leukemia-Lymphoma1ORPHANET
HgeneMLLT10C3163622Papillary Meningioma1CTD_human