FusionNeoAntigen Logo

Home

Download

Statistics

Examples

Help

Contact

Terms of Use

Center for Computational Systems Medicine
leaf

Fusion Gene and Fusion Protein Summary

leaf

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

leaf

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

leaf

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

leaf

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

leaf

Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)

leaf

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

leaf

Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)

leaf

Potential target of CAR-T therapy development

leaf

Information on the samples that have these potential fusion neoantigens

leaf

Fusion Protein Targeting Drugs - (Manual Curation)

leaf

Fusion Protein Related diseases - (Manual Curation)

Fusion Protein:DGKD-LAPTM5

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: DGKD-LAPTM5
FusionPDB ID: 22448
FusionGDB2.0 ID: 22448
HgeneTgene
Gene symbol

DGKD

LAPTM5

Gene ID

8527

7805

Gene namediacylglycerol kinase deltalysosomal protein transmembrane 5
SynonymsDGK-delta|DGKdelta|dgkd-2CLAST6
Cytomap

2q37.1

1p35.2

Type of geneprotein-codingprotein-coding
Descriptiondiacylglycerol kinase deltaDAG kinase deltadiacylglycerol kinase, delta 130kDadiglyceride kinase deltalysosomal-associated transmembrane protein 5CD40-ligand-activated specific transcriptshuman retinoic acid-inducible E3 proteinlysosomal associated multispanning membrane protein 5lysosomal multispanning membrane protein 5lysosomal-associated multitra
Modification date2020031320200313
UniProtAcc

Q16760

Main function of 5'-partner protein: FUNCTION: Diacylglycerol kinase that converts diacylglycerol/DAG into phosphatidic acid/phosphatidate/PA and regulates the respective levels of these two bioactive lipids (PubMed:12200442, PubMed:23949095). Thereby, acts as a central switch between the signaling pathways activated by these second messengers with different cellular targets and opposite effects in numerous biological processes (Probable). By controlling the levels of diacylglycerol, regulates for instance the PKC and EGF receptor signaling pathways and plays a crucial role during development (By similarity). May also regulate clathrin-dependent endocytosis (PubMed:17880279). {ECO:0000250|UniProtKB:E9PUQ8, ECO:0000269|PubMed:12200442, ECO:0000269|PubMed:17880279, ECO:0000269|PubMed:23949095, ECO:0000305}.

Q13571

Main function of 5'-partner protein: FUNCTION: May have a special functional role during embryogenesis and in adult hematopoietic cells. {ECO:0000269|PubMed:8661146}.
Ensembl transtripts involved in fusion geneENST idsENST00000264057, ENST00000409813, 
ENST00000489613, 
ENST00000476492, 
ENST00000294507, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score21 X 6 X 10=12607 X 4 X 5=140
# samples 2310
** MAII scorelog2(23/1260*10)=-2.4537179674429
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(10/140*10)=-0.485426827170242
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: DGKD [Title/Abstract] AND LAPTM5 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: DGKD [Title/Abstract] AND LAPTM5 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)DGKD(234299129)-LAPTM5(31215396), # samples:1
Anticipated loss of major functional domain due to fusion event.DGKD-LAPTM5 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.
DGKD-LAPTM5 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.
DGKD-LAPTM5 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.
DGKD-LAPTM5 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
HgeneDGKD

GO:0010033

response to organic substance

12200442



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/chr2:234299129/chr1:31215396)
- 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 DGKD (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 LAPTM5 (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)
ENST00000264057DGKDchr2234299129+ENST00000294507LAPTM5chr131215396-2421360121061349
ENST00000409813DGKDchr2234299129+ENST00000294507LAPTM5chr131215396-235629579996305

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
ENST00000264057ENST00000294507DGKDchr2234299129+LAPTM5chr131215396-0.0056386480.9943613
ENST00000409813ENST00000294507DGKDchr2234299129+LAPTM5chr131215396-0.0103676090.98963237

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

Top

Fusion Protein Breakpoint Sequences for DGKD-LAPTM5

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
DGKDchr2234299129LAPTM5chr13121539629572AESSTKNVNNSFTIMSVLLFIEHSVE
DGKDchr2234299129LAPTM5chr131215396360116AESSTKNVNNSFTIMSVLLFIEHSVE

Top

Potential FusionNeoAntigen Information of DGKD-LAPTM5 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.
DGKD-LAPTM5_234299129_31215396.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)
DGKD-LAPTM5chr2234299129chr131215396360HLA-B15:17FTIMSVLLF0.98010.89211120
DGKD-LAPTM5chr2234299129chr131215396360HLA-A02:21TIMSVLLFI0.97460.51051221
DGKD-LAPTM5chr2234299129chr131215396360HLA-B15:16FTIMSVLLF0.97070.85971120
DGKD-LAPTM5chr2234299129chr131215396360HLA-B58:02FTIMSVLLF0.90930.87591120
DGKD-LAPTM5chr2234299129chr131215396360HLA-B57:03FTIMSVLLF0.89590.96221120
DGKD-LAPTM5chr2234299129chr131215396360HLA-B51:07NSFTIMSV0.99820.7092917
DGKD-LAPTM5chr2234299129chr131215396360HLA-C03:08NSFTIMSVL0.99880.9072918
DGKD-LAPTM5chr2234299129chr131215396360HLA-C03:19NSFTIMSVL0.99840.9945918
DGKD-LAPTM5chr2234299129chr131215396360HLA-C15:06NSFTIMSVL0.99730.9435918
DGKD-LAPTM5chr2234299129chr131215396360HLA-C03:07NSFTIMSVL0.99730.9866918
DGKD-LAPTM5chr2234299129chr131215396360HLA-C12:12NSFTIMSVL0.94550.977918
DGKD-LAPTM5chr2234299129chr131215396360HLA-C15:04FTIMSVLLF0.93570.92511120
DGKD-LAPTM5chr2234299129chr131215396360HLA-C06:03NSFTIMSVL0.88280.9983918
DGKD-LAPTM5chr2234299129chr131215396360HLA-C12:04NSFTIMSVL0.8720.9981918
DGKD-LAPTM5chr2234299129chr131215396360HLA-C03:14FTIMSVLLF0.86420.98041120
DGKD-LAPTM5chr2234299129chr131215396360HLA-B51:07NNSFTIMSV0.67190.5307817
DGKD-LAPTM5chr2234299129chr131215396360HLA-C02:06NSFTIMSVL0.50960.9862918
DGKD-LAPTM5chr2234299129chr131215396360HLA-C14:03SFTIMSVL0.87970.9691018
DGKD-LAPTM5chr2234299129chr131215396360HLA-C14:02SFTIMSVL0.87970.9691018
DGKD-LAPTM5chr2234299129chr131215396360HLA-C03:03NSFTIMSVL0.99870.994918
DGKD-LAPTM5chr2234299129chr131215396360HLA-C03:04NSFTIMSVL0.99870.994918
DGKD-LAPTM5chr2234299129chr131215396360HLA-C03:17NSFTIMSVL0.99780.9813918
DGKD-LAPTM5chr2234299129chr131215396360HLA-C03:05NSFTIMSVL0.99770.9444918
DGKD-LAPTM5chr2234299129chr131215396360HLA-C15:02NSFTIMSVL0.99610.9234918
DGKD-LAPTM5chr2234299129chr131215396360HLA-C16:04NSFTIMSVL0.98710.9935918
DGKD-LAPTM5chr2234299129chr131215396360HLA-A68:02TIMSVLLFI0.97980.64691221
DGKD-LAPTM5chr2234299129chr131215396360HLA-C03:02FTIMSVLLF0.97590.97921120
DGKD-LAPTM5chr2234299129chr131215396360HLA-A02:06TIMSVLLFI0.97460.51051221
DGKD-LAPTM5chr2234299129chr131215396360HLA-A69:01TIMSVLLFI0.96840.59571221
DGKD-LAPTM5chr2234299129chr131215396360HLA-C12:03NSFTIMSVL0.95850.9937918
DGKD-LAPTM5chr2234299129chr131215396360HLA-B58:06FTIMSVLLF0.94960.87881120
DGKD-LAPTM5chr2234299129chr131215396360HLA-C12:02NSFTIMSVL0.94530.9897918
DGKD-LAPTM5chr2234299129chr131215396360HLA-C15:09FTIMSVLLF0.93570.92511120
DGKD-LAPTM5chr2234299129chr131215396360HLA-A25:01FTIMSVLLF0.88330.96551120
DGKD-LAPTM5chr2234299129chr131215396360HLA-C17:01NSFTIMSVL0.530.9686918
DGKD-LAPTM5chr2234299129chr131215396360HLA-C02:10FTIMSVLLF0.40970.99291120
DGKD-LAPTM5chr2234299129chr131215396360HLA-C02:02FTIMSVLLF0.40970.99291120
DGKD-LAPTM5chr2234299129chr131215396360HLA-C04:04SFTIMSVLL0.2340.89061019
DGKD-LAPTM5chr2234299129chr131215396360HLA-C14:02SFTIMSVLL0.07960.96631019
DGKD-LAPTM5chr2234299129chr131215396360HLA-C14:03SFTIMSVLL0.07960.96631019

Top

Potential FusionNeoAntigen Information of DGKD-LAPTM5 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)

Top

Fusion breakpoint peptide structures of DGKD-LAPTM5

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
6446NVNNSFTIMSVLLFDGKDLAPTM5chr2234299129chr131215396360

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of DGKD-LAPTM5

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-B14:023BVN6446NVNNSFTIMSVLLF-7.9962-8.1096
HLA-B14:023BVN6446NVNNSFTIMSVLLF-5.70842-6.74372
HLA-B52:013W396446NVNNSFTIMSVLLF-6.83737-6.95077
HLA-B52:013W396446NVNNSFTIMSVLLF-4.4836-5.5189
HLA-A11:014UQ26446NVNNSFTIMSVLLF-10.0067-10.1201
HLA-A11:014UQ26446NVNNSFTIMSVLLF-9.03915-10.0745
HLA-A24:025HGA6446NVNNSFTIMSVLLF-6.56204-6.67544
HLA-A24:025HGA6446NVNNSFTIMSVLLF-5.42271-6.45801
HLA-B44:053DX86446NVNNSFTIMSVLLF-7.85648-8.89178
HLA-B44:053DX86446NVNNSFTIMSVLLF-5.3978-5.5112
HLA-A02:016TDR6446NVNNSFTIMSVLLF-3.37154-4.40684

Top

Vaccine Design for the FusionNeoAntigens of DGKD-LAPTM5

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
DGKD-LAPTM5chr2234299129chr1312153961018SFTIMSVLAGTTTTACGATCATGAGCGTCTTG
DGKD-LAPTM5chr2234299129chr1312153961019SFTIMSVLLAGTTTTACGATCATGAGCGTCTTGTTG
DGKD-LAPTM5chr2234299129chr1312153961120FTIMSVLLFTTTACGATCATGAGCGTCTTGTTGTTC
DGKD-LAPTM5chr2234299129chr1312153961221TIMSVLLFIACGATCATGAGCGTCTTGTTGTTCATC
DGKD-LAPTM5chr2234299129chr131215396817NNSFTIMSVAACAACAGTTTTACGATCATGAGCGTC
DGKD-LAPTM5chr2234299129chr131215396917NSFTIMSVAACAGTTTTACGATCATGAGCGTC
DGKD-LAPTM5chr2234299129chr131215396918NSFTIMSVLAACAGTTTTACGATCATGAGCGTCTTG

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

Top

Information of the samples that have these potential fusion neoantigens of DGKD-LAPTM5

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
STADDGKD-LAPTM5chr2234299129ENST00000264057chr131215396ENST00000294507TCGA-BR-6453

Top

Potential target of CAR-T therapy development for DGKD-LAPTM5

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
TgeneLAPTM5chr2:234299129chr1:31215396ENST0000029450708134_1540263.0TransmembraneHelical
TgeneLAPTM5chr2:234299129chr1:31215396ENST0000029450708184_2040263.0TransmembraneHelical
TgeneLAPTM5chr2:234299129chr1:31215396ENST000002945070864_840263.0TransmembraneHelical
TgeneLAPTM5chr2:234299129chr1:31215396ENST000002945070892_1120263.0TransmembraneHelical

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

Top

Related Drugs to DGKD-LAPTM5

check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

Top

Related Diseases to DGKD-LAPTM5

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