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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:HMGA2-CHMP1A

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: HMGA2-CHMP1A
FusionPDB ID: 36825
FusionGDB2.0 ID: 36825
HgeneTgene
Gene symbol

HMGA2

CHMP1A

Gene ID

8091

5119

Gene namehigh mobility group AT-hook 2charged multivesicular body protein 1A
SynonymsBABL|HMGI-C|HMGIC|LIPO|STQTL9CHMP1|PCH8|PCOLN3|PRSM1|VPS46-1|VPS46A
Cytomap

12q14.3

16q24.3

Type of geneprotein-codingprotein-coding
Descriptionhigh mobility group protein HMGI-CHMGA2/KRT121P fusionhigh-mobility group (nonhistone chromosomal) protein isoform I-Ccharged multivesicular body protein 1acharged multivesicular body protein 1/chromatin modifying protein 1chromatin modifying protein 1Aprocollagen (type III) N-endopeptidaseprotease, metallo, 1, 33kDvacuolar protein sorting-associated protein 46-1
Modification date2020032920200313
UniProtAcc

P52926

Main function of 5'-partner protein: FUNCTION: Functions as a transcriptional regulator. Functions in cell cycle regulation through CCNA2. Plays an important role in chromosome condensation during the meiotic G2/M transition of spermatocytes. Plays a role in postnatal myogenesis, is involved in satellite cell activation (By similarity). Positively regulates IGF2 expression through PLAG1 and in a PLAG1-independent manner (PubMed:28796236). {ECO:0000250|UniProtKB:P52927, ECO:0000269|PubMed:14645522, ECO:0000269|PubMed:28796236}.

Q9HD42

Main function of 5'-partner protein: FUNCTION: Probable peripherally associated component of the endosomal sorting required for transport complex III (ESCRT-III) which is involved in multivesicular bodies (MVBs) formation and sorting of endosomal cargo proteins into MVBs. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. The MVB pathway appears to require the sequential function of ESCRT-O, -I,-II and -III complexes. ESCRT-III proteins mostly dissociate from the invaginating membrane before the ILV is released. The ESCRT machinery also functions in topologically equivalent membrane fission events, such as the terminal stages of cytokinesis and the budding of enveloped viruses (HIV-1 and other lentiviruses). ESCRT-III proteins are believed to mediate the necessary vesicle extrusion and/or membrane fission activities, possibly in conjunction with the AAA ATPase VPS4. Involved in cytokinesis. Involved in recruiting VPS4A and/or VPS4B to the midbody of dividing cells. May also be involved in chromosome condensation. Targets the Polycomb group (PcG) protein BMI1/PCGF4 to regions of condensed chromatin. May play a role in stable cell cycle progression and in PcG gene silencing. {ECO:0000269|PubMed:11559747, ECO:0000269|PubMed:11559748, ECO:0000269|PubMed:19129479, ECO:0000269|PubMed:23045692}.
Ensembl transtripts involved in fusion geneENST idsENST00000354636, ENST00000393577, 
ENST00000393578, ENST00000403681, 
ENST00000425208, ENST00000536545, 
ENST00000541363, 
ENST00000547614, 
ENST00000253475, ENST00000397901, 
ENST00000535997, ENST00000550102, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score43 X 25 X 15=1612545 X 11 X 21=10395
# samples 4348
** MAII scorelog2(43/16125*10)=-5.22881869049588
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(48/10395*10)=-4.43671154213721
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: HMGA2 [Title/Abstract] AND CHMP1A [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: HMGA2 [Title/Abstract] AND CHMP1A [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)HMGA2(66221867)-CHMP1A(89713739), # samples:1
Anticipated loss of major functional domain due to fusion event.HMGA2-CHMP1A 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.
HMGA2-CHMP1A 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.
HMGA2-CHMP1A 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.
HMGA2-CHMP1A 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.
HMGA2-CHMP1A seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
HMGA2-CHMP1A seems lost the major protein functional domain in Hgene partner, which is a transcription 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
HgeneHMGA2

GO:0000122

negative regulation of transcription by RNA polymerase II

14627817

HgeneHMGA2

GO:0002062

chondrocyte differentiation

21484705

HgeneHMGA2

GO:0006284

base-excision repair

19465398

HgeneHMGA2

GO:0007095

mitotic G2 DNA damage checkpoint

16061642

HgeneHMGA2

GO:0010564

regulation of cell cycle process

14645522

HgeneHMGA2

GO:0010628

positive regulation of gene expression

18832382

HgeneHMGA2

GO:0031052

chromosome breakage

19549901

HgeneHMGA2

GO:0031507

heterochromatin assembly

16901784

HgeneHMGA2

GO:0035978

histone H2A-S139 phosphorylation

16061642

HgeneHMGA2

GO:0035986

senescence-associated heterochromatin focus assembly

16901784

HgeneHMGA2

GO:0035988

chondrocyte proliferation

21484705

HgeneHMGA2

GO:0042769

DNA damage response, detection of DNA damage

19465398

HgeneHMGA2

GO:0043065

positive regulation of apoptotic process

16061642

HgeneHMGA2

GO:0043066

negative regulation of apoptotic process

19465398

HgeneHMGA2

GO:0043392

negative regulation of DNA binding

14645522

HgeneHMGA2

GO:0043922

negative regulation by host of viral transcription

17005673

HgeneHMGA2

GO:0045869

negative regulation of single stranded viral RNA replication via double stranded DNA intermediate

17005673

HgeneHMGA2

GO:0045892

negative regulation of transcription, DNA-templated

18832382

HgeneHMGA2

GO:0045893

positive regulation of transcription, DNA-templated

15225648|15755872|17005673|17324944|17426251

HgeneHMGA2

GO:0045944

positive regulation of transcription by RNA polymerase II

14645522|18832382

HgeneHMGA2

GO:0071158

positive regulation of cell cycle arrest

16061642

HgeneHMGA2

GO:0071902

positive regulation of protein serine/threonine kinase activity

19549901

HgeneHMGA2

GO:0090402

oncogene-induced cell senescence

16901784

HgeneHMGA2

GO:2000648

positive regulation of stem cell proliferation

21484705

HgeneHMGA2

GO:2000679

positive regulation of transcription regulatory region DNA binding

18832382

HgeneHMGA2

GO:2000685

positive regulation of cellular response to X-ray

16061642

HgeneHMGA2

GO:2001022

positive regulation of response to DNA damage stimulus

16061642|19465398

HgeneHMGA2

GO:2001033

negative regulation of double-strand break repair via nonhomologous end joining

19549901

HgeneHMGA2

GO:2001038

regulation of cellular response to drug

16061642

TgeneCHMP1A

GO:0007076

mitotic chromosome condensation

11559747

TgeneCHMP1A

GO:0016192

vesicle-mediated transport

11559748

TgeneCHMP1A

GO:0016458

gene silencing

11559747

TgeneCHMP1A

GO:0045892

negative regulation of transcription, DNA-templated

11559747



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/chr12:66221867/chr16:89713739)
- 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 HMGA2 (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 CHMP1A (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)
ENST00000403681HMGA2chr1266221867+ENST00000397901CHMP1Achr1689713739-33121338114992292
ENST00000403681HMGA2chr1266221867+ENST00000535997CHMP1Achr1689713739-32801338114992292
ENST00000403681HMGA2chr1266221867+ENST00000550102CHMP1Achr1689713739-18541338114992292
ENST00000541363HMGA2chr1266221867+ENST00000397901CHMP1Achr1689713739-2545571373909178
ENST00000541363HMGA2chr1266221867+ENST00000535997CHMP1Achr1689713739-2513571373909178
ENST00000541363HMGA2chr1266221867+ENST00000550102CHMP1Achr1689713739-1087571373909178
ENST00000393577HMGA2chr1266221867+ENST00000397901CHMP1Achr1689713739-2320346148684178
ENST00000393577HMGA2chr1266221867+ENST00000535997CHMP1Achr1689713739-2288346148684178
ENST00000393577HMGA2chr1266221867+ENST00000550102CHMP1Achr1689713739-862346148684178
ENST00000393578HMGA2chr1266221867+ENST00000397901CHMP1Achr1689713739-298310091663220
ENST00000393578HMGA2chr1266221867+ENST00000535997CHMP1Achr1689713739-295110091663220
ENST00000393578HMGA2chr1266221867+ENST00000550102CHMP1Achr1689713739-152510091663220
ENST00000425208HMGA2chr1266221867+ENST00000397901CHMP1Achr1689713739-298310091663220
ENST00000425208HMGA2chr1266221867+ENST00000535997CHMP1Achr1689713739-295110091663220
ENST00000425208HMGA2chr1266221867+ENST00000550102CHMP1Achr1689713739-152510091663220
ENST00000536545HMGA2chr1266221867+ENST00000397901CHMP1Achr1689713739-298310091663220
ENST00000536545HMGA2chr1266221867+ENST00000535997CHMP1Achr1689713739-295110091663220
ENST00000536545HMGA2chr1266221867+ENST00000550102CHMP1Achr1689713739-152510091663220
ENST00000354636HMGA2chr1266221867+ENST00000397901CHMP1Achr1689713739-298310091663220
ENST00000354636HMGA2chr1266221867+ENST00000535997CHMP1Achr1689713739-295110091663220
ENST00000354636HMGA2chr1266221867+ENST00000550102CHMP1Achr1689713739-152510091663220

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
ENST00000403681ENST00000397901HMGA2chr1266221867+CHMP1Achr1689713739-0.0057744590.99422556
ENST00000403681ENST00000535997HMGA2chr1266221867+CHMP1Achr1689713739-0.0068093380.9931907
ENST00000403681ENST00000550102HMGA2chr1266221867+CHMP1Achr1689713739-0.0036575490.9963425
ENST00000541363ENST00000397901HMGA2chr1266221867+CHMP1Achr1689713739-0.0093928070.99060714
ENST00000541363ENST00000535997HMGA2chr1266221867+CHMP1Achr1689713739-0.0104214420.98957855
ENST00000541363ENST00000550102HMGA2chr1266221867+CHMP1Achr1689713739-0.0029209280.99707913
ENST00000393577ENST00000397901HMGA2chr1266221867+CHMP1Achr1689713739-0.009879180.9901209
ENST00000393577ENST00000535997HMGA2chr1266221867+CHMP1Achr1689713739-0.0095890520.9904109
ENST00000393577ENST00000550102HMGA2chr1266221867+CHMP1Achr1689713739-0.0038863110.99611366
ENST00000393578ENST00000397901HMGA2chr1266221867+CHMP1Achr1689713739-0.0032593470.99674064
ENST00000393578ENST00000535997HMGA2chr1266221867+CHMP1Achr1689713739-0.0034900010.99650997
ENST00000393578ENST00000550102HMGA2chr1266221867+CHMP1Achr1689713739-0.0028032110.9971968
ENST00000425208ENST00000397901HMGA2chr1266221867+CHMP1Achr1689713739-0.0032593470.99674064
ENST00000425208ENST00000535997HMGA2chr1266221867+CHMP1Achr1689713739-0.0034900010.99650997
ENST00000425208ENST00000550102HMGA2chr1266221867+CHMP1Achr1689713739-0.0028032110.9971968
ENST00000536545ENST00000397901HMGA2chr1266221867+CHMP1Achr1689713739-0.0032593470.99674064
ENST00000536545ENST00000535997HMGA2chr1266221867+CHMP1Achr1689713739-0.0034900010.99650997
ENST00000536545ENST00000550102HMGA2chr1266221867+CHMP1Achr1689713739-0.0028032110.9971968
ENST00000354636ENST00000397901HMGA2chr1266221867+CHMP1Achr1689713739-0.0032593470.99674064
ENST00000354636ENST00000535997HMGA2chr1266221867+CHMP1Achr1689713739-0.0034900010.99650997
ENST00000354636ENST00000550102HMGA2chr1266221867+CHMP1Achr1689713739-0.0028032110.9971968

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 HMGA2-CHMP1A

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
HMGA2chr1266221867CHMP1Achr168971373934666GSKNKSPSKAAQKVTKNMAQVTKALD
HMGA2chr1266221867CHMP1Achr168971373957166GSKNKSPSKAAQKVTKNMAQVTKALD

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Potential FusionNeoAntigen Information of HMGA2-CHMP1A 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.
HMGA2-CHMP1A_66221867_89713739.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)
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-B35:04SPSKAAQKV0.63650.8881514
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-B35:02SPSKAAQKV0.63650.8881514
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-B35:03SPSKAAQKV0.57960.8118514
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-B15:04AQKVTKNM0.9920.89911018
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-C03:08AAQKVTKNM0.99840.8921918
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-C15:04AAQKVTKNM0.99780.9114918
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-C03:19AAQKVTKNM0.9950.9786918
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-C03:07AAQKVTKNM0.99390.9706918
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-C15:06AAQKVTKNM0.98750.9275918
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-C12:12AAQKVTKNM0.98390.9442918
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-C06:03AAQKVTKNM0.94160.9923918
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-C12:04AAQKVTKNM0.92960.991918
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-B51:07SPSKAAQKV0.74490.7017514
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-B15:04AQKVTKNMA0.67560.91111019
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-B35:12SPSKAAQKV0.63650.8881514
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-B39:10SPSKAAQKV0.08910.7763514
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-B15:68AQKVTKNM0.98450.57761018
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-C03:03AAQKVTKNM0.99850.979918
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-C03:04AAQKVTKNM0.99850.979918
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-C03:02AAQKVTKNM0.99820.969918
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-C15:09AAQKVTKNM0.99780.9114918
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-C03:05AAQKVTKNM0.99220.9052918
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-C03:17AAQKVTKNM0.98990.9662918
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-C12:03AAQKVTKNM0.98240.9796918
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-C12:02AAQKVTKNM0.9730.9685918
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-C16:04AAQKVTKNM0.93480.9795918
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-C02:10AAQKVTKNM0.88740.9748918
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-C02:02AAQKVTKNM0.88740.9748918
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-C16:01AAQKVTKNM0.74310.9808918
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-C16:02AAQKVTKNM0.69530.9917918
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-B35:09SPSKAAQKV0.63650.8881514
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-B07:13AAQKVTKNM0.5920.8616918
HMGA2-CHMP1Achr1266221867chr1689713739346HLA-B67:01SPSKAAQKV0.2030.5806514

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Potential FusionNeoAntigen Information of HMGA2-CHMP1A 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.
HMGA2-CHMP1A_66221867_89713739.msa

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)
HMGA2-CHMP1Achr1266221867chr1689713739346DRB3-0201AAQKVTKNMAQVTKA924
HMGA2-CHMP1Achr1266221867chr1689713739346DRB3-0201AQKVTKNMAQVTKAL1025
HMGA2-CHMP1Achr1266221867chr1689713739346DRB3-0202AAQKVTKNMAQVTKA924
HMGA2-CHMP1Achr1266221867chr1689713739346DRB3-0204AAQKVTKNMAQVTKA924
HMGA2-CHMP1Achr1266221867chr1689713739346DRB3-0204AQKVTKNMAQVTKAL1025
HMGA2-CHMP1Achr1266221867chr1689713739346DRB3-0210AAQKVTKNMAQVTKA924
HMGA2-CHMP1Achr1266221867chr1689713739346DRB3-0211AAQKVTKNMAQVTKA924
HMGA2-CHMP1Achr1266221867chr1689713739346DRB3-0214AAQKVTKNMAQVTKA924
HMGA2-CHMP1Achr1266221867chr1689713739346DRB3-0214AQKVTKNMAQVTKAL1025
HMGA2-CHMP1Achr1266221867chr1689713739346DRB3-0218AAQKVTKNMAQVTKA924
HMGA2-CHMP1Achr1266221867chr1689713739346DRB3-0220AAQKVTKNMAQVTKA924
HMGA2-CHMP1Achr1266221867chr1689713739346DRB3-0223AAQKVTKNMAQVTKA924
HMGA2-CHMP1Achr1266221867chr1689713739346DRB3-0224AAQKVTKNMAQVTKA924
HMGA2-CHMP1Achr1266221867chr1689713739346DRB3-0224AQKVTKNMAQVTKAL1025
HMGA2-CHMP1Achr1266221867chr1689713739346DRB3-0225AAQKVTKNMAQVTKA924
HMGA2-CHMP1Achr1266221867chr1689713739346DRB3-0301AAQKVTKNMAQVTKA924
HMGA2-CHMP1Achr1266221867chr1689713739346DRB3-0301AQKVTKNMAQVTKAL1025

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Fusion breakpoint peptide structures of HMGA2-CHMP1A

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
6989PSKAAQKVTKNMAQHMGA2CHMP1Achr1266221867chr1689713739346

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of HMGA2-CHMP1A

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-B14:023BVN6989PSKAAQKVTKNMAQ-6.12283-6.12283
HLA-A24:025HGA6989PSKAAQKVTKNMAQ-7.36995-7.36995

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Vaccine Design for the FusionNeoAntigens of HMGA2-CHMP1A

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
HMGA2-CHMP1Achr1266221867chr16897137391018AQKVTKNMGCTCAAAAGGTGACCAAGAATATG
HMGA2-CHMP1Achr1266221867chr16897137391019AQKVTKNMAGCTCAAAAGGTGACCAAGAATATGGCC
HMGA2-CHMP1Achr1266221867chr1689713739514SPSKAAQKVAGTCCCTCTAAAGCAGCTCAAAAGGTG
HMGA2-CHMP1Achr1266221867chr1689713739918AAQKVTKNMGCAGCTCAAAAGGTGACCAAGAATATG

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
HMGA2-CHMP1Achr1266221867chr16897137391025AQKVTKNMAQVTKALGCTCAAAAGGTGACCAAGAATATGGCCCAGGTGACCAAAGCCCTG
HMGA2-CHMP1Achr1266221867chr1689713739924AAQKVTKNMAQVTKAGCAGCTCAAAAGGTGACCAAGAATATGGCCCAGGTGACCAAAGCC

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Information of the samples that have these potential fusion neoantigens of HMGA2-CHMP1A

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
KIRCHMGA2-CHMP1Achr1266221867ENST00000393577chr1689713739ENST00000397901TCGA-B0-4698-01A

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Potential target of CAR-T therapy development for HMGA2-CHMP1A

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 HMGA2-CHMP1A

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 HMGA2-CHMP1A

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
HgeneHMGA2C1519176Salivary Gland Pleomorphic Adenoma2ORPHANET
HgeneHMGA2C0005612Birth Weight1CTD_human
HgeneHMGA2C0006826Malignant Neoplasms1CTD_human
HgeneHMGA2C0027626Neoplasm Invasiveness1CTD_human
HgeneHMGA2C0027651Neoplasms1CTD_human
HgeneHMGA2C0086692Benign Neoplasm1CTD_human
HgeneHMGA2C0175693Russell-Silver syndrome1GENOMICS_ENGLAND
HgeneHMGA2C0473935Radiolabeled somatostatin analog study1GENOMICS_ENGLAND
HgeneHMGA2C0796160MENTAL RETARDATION, X-LINKED, SNYDER-ROBINSON TYPE1GENOMICS_ENGLAND
HgeneHMGA2C1096309Myolipoma1GENOMICS_ENGLAND
HgeneHMGA2C430514012q14 microdeletion syndrome1ORPHANET