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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:PHC3-GNA12

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PHC3-GNA12
FusionPDB ID: 64742
FusionGDB2.0 ID: 64742
HgeneTgene
Gene symbol

PHC3

GNA12

Gene ID

80012

2768

Gene namepolyhomeotic homolog 3G protein subunit alpha 12
SynonymsEDR3|HPH3NNX3|RMP|gep
Cytomap

3q26.2

7p22.3-p22.2

Type of geneprotein-codingprotein-coding
Descriptionpolyhomeotic-like protein 3early development regulator 3early development regulatory protein 3homolog of polyhomeotic 3polyhomeotic like 3guanine nucleotide-binding protein subunit alpha-12WUGSC:H_GS165O14.2g alpha-12guanine nucleotide binding protein (G protein) alpha 12
Modification date2020031320200313
UniProtAcc.

Q03113

Main function of 5'-partner protein: FUNCTION: Guanine nucleotide-binding proteins (G proteins) are involved as modulators or transducers in various transmembrane signaling systems (PubMed:22609986, PubMed:15525651, PubMed:15240885, PubMed:17565996, PubMed:12515866, PubMed:16787920, PubMed:16705036, PubMed:23762476, PubMed:27084452). Activates effector molecule RhoA by binding and activating RhoGEFs (ARHGEF12/LARG) (PubMed:15240885, PubMed:12515866, PubMed:16202387). GNA12-dependent Rho signaling subsequently regulates transcription factor AP-1 (activating protein-1) (By similarity). GNA12-dependent Rho signaling also regulates protein phosphatese 2A activation causing dephosphorylation of its target proteins (PubMed:15525651, PubMed:17565996). Promotes tumor cell invasion and metastasis by activating RhoA/ROCK signaling pathway and up-regulating proinflammatory cytokine production (PubMed:23762476, PubMed:16787920, PubMed:16705036, PubMed:27084452). Inhibits CDH1-mediated cell adhesion in process independent from Rho activation (PubMed:11976333, PubMed:16787920). Together with NAPA promotes CDH5 localization to plasma membrane (PubMed:15980433). May play a role in the control of cell migration through the TOR signaling cascade (PubMed:22609986). {ECO:0000250|UniProtKB:P27600, ECO:0000269|PubMed:11976333, ECO:0000269|PubMed:12515866, ECO:0000269|PubMed:15240885, ECO:0000269|PubMed:15525651, ECO:0000269|PubMed:15980433, ECO:0000269|PubMed:16705036, ECO:0000269|PubMed:16787920, ECO:0000269|PubMed:17565996, ECO:0000269|PubMed:22609986, ECO:0000269|PubMed:23762476, ECO:0000269|PubMed:27084452}.
Ensembl transtripts involved in fusion geneENST idsENST00000467570, ENST00000474275, 
ENST00000481639, ENST00000494943, 
ENST00000495893, ENST00000497658, 
ENST00000396960, ENST00000407653, 
ENST00000407904, ENST00000491117, 
ENST00000275364, ENST00000544127, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score15 X 15 X 11=24757 X 6 X 4=168
# samples 209
** MAII scorelog2(20/2475*10)=-3.62935662007961
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/168*10)=-0.900464326449086
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: PHC3 [Title/Abstract] AND GNA12 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: PHC3 [Title/Abstract] AND GNA12 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)GNA12(2883487)-PHC3(169896726), # samples:3
PHC3(169896561)-GNA12(2834777), # samples:1
Anticipated loss of major functional domain due to fusion event.PHC3-GNA12 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.
PHC3-GNA12 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.
PHC3-GNA12 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.
PHC3-GNA12 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.
GNA12-PHC3 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF.
GNA12-PHC3 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
GNA12-PHC3 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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


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/chr3:2883487/chr7:169896726)
- 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 PHC3 (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 GNA12 (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)
ENST00000495893PHC3chr3169896561-ENST00000275364GNA12chr72834777-4118212321048338
ENST00000495893PHC3chr3169896561-ENST00000544127GNA12chr72834777-136521232997321
ENST00000494943PHC3chr3169896561-ENST00000275364GNA12chr72834777-4119213691049326
ENST00000494943PHC3chr3169896561-ENST00000544127GNA12chr72834777-136621369998309
ENST00000467570PHC3chr3169896561-ENST00000275364GNA12chr72834777-4120214341050338
ENST00000467570PHC3chr3169896561-ENST00000544127GNA12chr72834777-136721434999321
ENST00000474275PHC3chr3169896561-ENST00000275364GNA12chr72834777-4114208641044326
ENST00000474275PHC3chr3169896561-ENST00000544127GNA12chr72834777-136120864993309
ENST00000497658PHC3chr3169896561-ENST00000275364GNA12chr72834777-4104198181034338
ENST00000497658PHC3chr3169896561-ENST00000544127GNA12chr72834777-135119818983321
ENST00000481639PHC3chr3169896561-ENST00000275364GNA12chr72834777-4118212321048338
ENST00000481639PHC3chr3169896561-ENST00000544127GNA12chr72834777-136521232997321

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
ENST00000495893ENST00000275364PHC3chr3169896561-GNA12chr72834777-0.0027772220.9972228
ENST00000495893ENST00000544127PHC3chr3169896561-GNA12chr72834777-0.0029794770.99702054
ENST00000494943ENST00000275364PHC3chr3169896561-GNA12chr72834777-0.0029129630.99708706
ENST00000494943ENST00000544127PHC3chr3169896561-GNA12chr72834777-0.0049369870.995063
ENST00000467570ENST00000275364PHC3chr3169896561-GNA12chr72834777-0.0027797490.9972203
ENST00000467570ENST00000544127PHC3chr3169896561-GNA12chr72834777-0.002864790.99713516
ENST00000474275ENST00000275364PHC3chr3169896561-GNA12chr72834777-0.0029156670.9970843
ENST00000474275ENST00000544127PHC3chr3169896561-GNA12chr72834777-0.0049498620.99505013
ENST00000497658ENST00000275364PHC3chr3169896561-GNA12chr72834777-0.0028040170.99719596
ENST00000497658ENST00000544127PHC3chr3169896561-GNA12chr72834777-0.0033073980.99669254
ENST00000481639ENST00000275364PHC3chr3169896561-GNA12chr72834777-0.0027772220.9972228
ENST00000481639ENST00000544127PHC3chr3169896561-GNA12chr72834777-0.0029794770.99702054

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 PHC3-GNA12

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
PHC3chr3169896561GNA12chr7283477719860ISVYSGSDRHAVQGSRVLVDARDKLG
PHC3chr3169896561GNA12chr7283477720848ISVYSGSDRHAVQGSRVLVDARDKLG
PHC3chr3169896561GNA12chr7283477721260ISVYSGSDRHAVQGSRVLVDARDKLG
PHC3chr3169896561GNA12chr7283477721348ISVYSGSDRHAVQGSRVLVDARDKLG
PHC3chr3169896561GNA12chr7283477721460ISVYSGSDRHAVQGSRVLVDARDKLG

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Potential FusionNeoAntigen Information of PHC3-GNA12 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.
PHC3-GNA12_169896561_2834777.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)
PHC3-GNA12chr3169896561chr72834777214HLA-B15:10HAVQGSRVL0.98940.5553918
PHC3-GNA12chr3169896561chr72834777214HLA-B38:01RHAVQGSRV0.97870.8329817
PHC3-GNA12chr3169896561chr72834777214HLA-B38:02RHAVQGSRV0.97760.8408817
PHC3-GNA12chr3169896561chr72834777214HLA-B35:03HAVQGSRVL0.96750.8757918
PHC3-GNA12chr3169896561chr72834777214HLA-B14:01HAVQGSRVL0.96310.8124918
PHC3-GNA12chr3169896561chr72834777214HLA-B14:02HAVQGSRVL0.96310.8124918
PHC3-GNA12chr3169896561chr72834777214HLA-B07:10HAVQGSRVL0.95610.6072918
PHC3-GNA12chr3169896561chr72834777214HLA-B15:37HAVQGSRVL0.9540.6482918
PHC3-GNA12chr3169896561chr72834777214HLA-B35:05HAVQGSRVL0.92670.6961918
PHC3-GNA12chr3169896561chr72834777214HLA-B35:04HAVQGSRVL0.92240.9502918
PHC3-GNA12chr3169896561chr72834777214HLA-B35:02HAVQGSRVL0.92240.9502918
PHC3-GNA12chr3169896561chr72834777214HLA-A30:08AVQGSRVLV0.90290.70871019
PHC3-GNA12chr3169896561chr72834777214HLA-B39:01RHAVQGSRVL0.99050.7966818
PHC3-GNA12chr3169896561chr72834777214HLA-B38:01RHAVQGSRVL0.97570.9065818
PHC3-GNA12chr3169896561chr72834777214HLA-B38:02RHAVQGSRVL0.97470.9113818
PHC3-GNA12chr3169896561chr72834777214HLA-B15:10RHAVQGSRVL0.88930.573818
PHC3-GNA12chr3169896561chr72834777214HLA-B07:10RHAVQGSRVL0.86710.635818
PHC3-GNA12chr3169896561chr72834777214HLA-B15:37RHAVQGSRVL0.43090.6772818
PHC3-GNA12chr3169896561chr72834777214HLA-B14:01DRHAVQGSRVL0.9980.7246718
PHC3-GNA12chr3169896561chr72834777214HLA-B14:02DRHAVQGSRVL0.9980.7246718
PHC3-GNA12chr3169896561chr72834777214HLA-C03:19HAVQGSRVL0.99970.9877918
PHC3-GNA12chr3169896561chr72834777214HLA-C03:08HAVQGSRVL0.99960.9067918
PHC3-GNA12chr3169896561chr72834777214HLA-C03:07HAVQGSRVL0.99960.972918
PHC3-GNA12chr3169896561chr72834777214HLA-C15:04HAVQGSRVL0.99940.946918
PHC3-GNA12chr3169896561chr72834777214HLA-C15:06HAVQGSRVL0.99890.9491918
PHC3-GNA12chr3169896561chr72834777214HLA-C08:13HAVQGSRVL0.99270.9749918
PHC3-GNA12chr3169896561chr72834777214HLA-C08:04HAVQGSRVL0.99270.9749918
PHC3-GNA12chr3169896561chr72834777214HLA-C04:06HAVQGSRVL0.99240.949918
PHC3-GNA12chr3169896561chr72834777214HLA-B39:05RHAVQGSRV0.97690.6711817
PHC3-GNA12chr3169896561chr72834777214HLA-C12:12HAVQGSRVL0.97520.9563918
PHC3-GNA12chr3169896561chr72834777214HLA-C12:16HAVQGSRVL0.96320.9736918
PHC3-GNA12chr3169896561chr72834777214HLA-C08:03HAVQGSRVL0.95520.9863918
PHC3-GNA12chr3169896561chr72834777214HLA-B39:10HAVQGSRVL0.9540.8586918
PHC3-GNA12chr3169896561chr72834777214HLA-C06:03HAVQGSRVL0.9490.9937918
PHC3-GNA12chr3169896561chr72834777214HLA-C12:04HAVQGSRVL0.94510.9933918
PHC3-GNA12chr3169896561chr72834777214HLA-C03:14HAVQGSRVL0.92340.9868918
PHC3-GNA12chr3169896561chr72834777214HLA-B35:12HAVQGSRVL0.92240.9502918
PHC3-GNA12chr3169896561chr72834777214HLA-C01:17HAVQGSRVL0.91680.9709918
PHC3-GNA12chr3169896561chr72834777214HLA-B07:12HAVQGSRVL0.89610.7218918
PHC3-GNA12chr3169896561chr72834777214HLA-C02:06HAVQGSRVL0.78360.9729918
PHC3-GNA12chr3169896561chr72834777214HLA-C01:30HAVQGSRVL0.56150.9656918
PHC3-GNA12chr3169896561chr72834777214HLA-B39:05RHAVQGSRVL0.96980.7694818
PHC3-GNA12chr3169896561chr72834777214HLA-C03:04HAVQGSRVL0.99970.9879918
PHC3-GNA12chr3169896561chr72834777214HLA-C03:03HAVQGSRVL0.99970.9879918
PHC3-GNA12chr3169896561chr72834777214HLA-C03:67HAVQGSRVL0.99970.9792918
PHC3-GNA12chr3169896561chr72834777214HLA-C03:05HAVQGSRVL0.99950.9345918
PHC3-GNA12chr3169896561chr72834777214HLA-C03:17HAVQGSRVL0.99940.9809918
PHC3-GNA12chr3169896561chr72834777214HLA-C15:09HAVQGSRVL0.99940.946918
PHC3-GNA12chr3169896561chr72834777214HLA-C03:02HAVQGSRVL0.99890.978918
PHC3-GNA12chr3169896561chr72834777214HLA-C15:05HAVQGSRVL0.99860.919918
PHC3-GNA12chr3169896561chr72834777214HLA-C15:02HAVQGSRVL0.99790.8976918
PHC3-GNA12chr3169896561chr72834777214HLA-B35:11HAVQGSRVL0.98960.8542918
PHC3-GNA12chr3169896561chr72834777214HLA-C16:04HAVQGSRVL0.98950.9739918
PHC3-GNA12chr3169896561chr72834777214HLA-C06:06HAVQGSRVL0.98310.9932918
PHC3-GNA12chr3169896561chr72834777214HLA-C03:06HAVQGSRVL0.98150.9897918
PHC3-GNA12chr3169896561chr72834777214HLA-B38:05RHAVQGSRV0.97870.8329817
PHC3-GNA12chr3169896561chr72834777214HLA-C12:03HAVQGSRVL0.97570.985918
PHC3-GNA12chr3169896561chr72834777214HLA-C12:02HAVQGSRVL0.97360.9771918
PHC3-GNA12chr3169896561chr72834777214HLA-B35:13HAVQGSRVL0.9710.8825918
PHC3-GNA12chr3169896561chr72834777214HLA-B07:13HAVQGSRVL0.9710.9058918
PHC3-GNA12chr3169896561chr72834777214HLA-C08:01HAVQGSRVL0.95520.9863918
PHC3-GNA12chr3169896561chr72834777214HLA-B35:23HAVQGSRVL0.9450.8694918
PHC3-GNA12chr3169896561chr72834777214HLA-C06:02HAVQGSRVL0.93350.9931918
PHC3-GNA12chr3169896561chr72834777214HLA-C06:17HAVQGSRVL0.93350.9931918
PHC3-GNA12chr3169896561chr72834777214HLA-B35:30HAVQGSRVL0.92370.8159918
PHC3-GNA12chr3169896561chr72834777214HLA-B35:17HAVQGSRVL0.92370.8159918
PHC3-GNA12chr3169896561chr72834777214HLA-B35:09HAVQGSRVL0.92240.9502918
PHC3-GNA12chr3169896561chr72834777214HLA-C01:02HAVQGSRVL0.89980.9687918
PHC3-GNA12chr3169896561chr72834777214HLA-C16:01HAVQGSRVL0.8580.9803918
PHC3-GNA12chr3169896561chr72834777214HLA-B15:09HAVQGSRVL0.85670.6772918
PHC3-GNA12chr3169896561chr72834777214HLA-B15:30HAVQGSRVL0.82020.9176918
PHC3-GNA12chr3169896561chr72834777214HLA-C16:02HAVQGSRVL0.8170.9926918
PHC3-GNA12chr3169896561chr72834777214HLA-C02:10HAVQGSRVL0.8150.9826918
PHC3-GNA12chr3169896561chr72834777214HLA-C02:02HAVQGSRVL0.8150.9826918
PHC3-GNA12chr3169896561chr72834777214HLA-B15:08HAVQGSRVL0.80480.8721918
PHC3-GNA12chr3169896561chr72834777214HLA-B35:43HAVQGSRVL0.78730.877918
PHC3-GNA12chr3169896561chr72834777214HLA-C01:03HAVQGSRVL0.76030.9606918
PHC3-GNA12chr3169896561chr72834777214HLA-C06:08HAVQGSRVL0.73670.9905918
PHC3-GNA12chr3169896561chr72834777214HLA-B78:02HAVQGSRVL0.59160.5694918
PHC3-GNA12chr3169896561chr72834777214HLA-B15:09RHAVQGSRV0.58680.6361817
PHC3-GNA12chr3169896561chr72834777214HLA-B39:11RHAVQGSRV0.49990.5541817
PHC3-GNA12chr3169896561chr72834777214HLA-C17:01HAVQGSRVL0.38040.9736918
PHC3-GNA12chr3169896561chr72834777214HLA-B38:05RHAVQGSRVL0.97570.9065818
PHC3-GNA12chr3169896561chr72834777214HLA-B39:11RHAVQGSRVL0.79760.7342818
PHC3-GNA12chr3169896561chr72834777214HLA-B15:09RHAVQGSRVL0.73030.6407818

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Potential FusionNeoAntigen Information of PHC3-GNA12 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.
PHC3-GNA12_169896561_2834777.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)
PHC3-GNA12chr3169896561chr72834777214DRB1-0301VQGSRVLVDARDKLG1126
PHC3-GNA12chr3169896561chr72834777214DRB1-0303VQGSRVLVDARDKLG1126
PHC3-GNA12chr3169896561chr72834777214DRB1-0307VQGSRVLVDARDKLG1126
PHC3-GNA12chr3169896561chr72834777214DRB1-0310VQGSRVLVDARDKLG1126
PHC3-GNA12chr3169896561chr72834777214DRB1-0310AVQGSRVLVDARDKL1025
PHC3-GNA12chr3169896561chr72834777214DRB1-0313VQGSRVLVDARDKLG1126
PHC3-GNA12chr3169896561chr72834777214DRB1-0315VQGSRVLVDARDKLG1126
PHC3-GNA12chr3169896561chr72834777214DRB1-0318VQGSRVLVDARDKLG1126
PHC3-GNA12chr3169896561chr72834777214DRB1-0320VQGSRVLVDARDKLG1126
PHC3-GNA12chr3169896561chr72834777214DRB1-0322VQGSRVLVDARDKLG1126
PHC3-GNA12chr3169896561chr72834777214DRB1-0324VQGSRVLVDARDKLG1126
PHC3-GNA12chr3169896561chr72834777214DRB1-0326VQGSRVLVDARDKLG1126
PHC3-GNA12chr3169896561chr72834777214DRB1-0328VQGSRVLVDARDKLG1126
PHC3-GNA12chr3169896561chr72834777214DRB1-0330VQGSRVLVDARDKLG1126
PHC3-GNA12chr3169896561chr72834777214DRB1-0332VQGSRVLVDARDKLG1126
PHC3-GNA12chr3169896561chr72834777214DRB1-0334VQGSRVLVDARDKLG1126
PHC3-GNA12chr3169896561chr72834777214DRB1-0336VQGSRVLVDARDKLG1126
PHC3-GNA12chr3169896561chr72834777214DRB1-0342VQGSRVLVDARDKLG1126
PHC3-GNA12chr3169896561chr72834777214DRB1-0344VQGSRVLVDARDKLG1126
PHC3-GNA12chr3169896561chr72834777214DRB1-0346VQGSRVLVDARDKLG1126
PHC3-GNA12chr3169896561chr72834777214DRB1-0348VQGSRVLVDARDKLG1126
PHC3-GNA12chr3169896561chr72834777214DRB1-0350VQGSRVLVDARDKLG1126
PHC3-GNA12chr3169896561chr72834777214DRB1-0352VQGSRVLVDARDKLG1126
PHC3-GNA12chr3169896561chr72834777214DRB1-0354VQGSRVLVDARDKLG1126
PHC3-GNA12chr3169896561chr72834777214DRB1-1107VQGSRVLVDARDKLG1126
PHC3-GNA12chr3169896561chr72834777214DRB1-1394VQGSRVLVDARDKLG1126
PHC3-GNA12chr3169896561chr72834777214DRB1-1407ISVYSGSDRHAVQGS015
PHC3-GNA12chr3169896561chr72834777214DRB1-1414ISVYSGSDRHAVQGS015
PHC3-GNA12chr3169896561chr72834777214DRB1-1436ISVYSGSDRHAVQGS015
PHC3-GNA12chr3169896561chr72834777214DRB1-1442ISVYSGSDRHAVQGS015
PHC3-GNA12chr3169896561chr72834777214DRB1-1444ISVYSGSDRHAVQGS015
PHC3-GNA12chr3169896561chr72834777214DRB1-1476VQGSRVLVDARDKLG1126
PHC3-GNA12chr3169896561chr72834777214DRB1-1479VQGSRVLVDARDKLG1126

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Fusion breakpoint peptide structures of PHC3-GNA12

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
8484SDRHAVQGSRVLVDPHC3GNA12chr3169896561chr72834777214

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PHC3-GNA12

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-B14:023BVN8484SDRHAVQGSRVLVD-7.15543-7.26883
HLA-B14:023BVN8484SDRHAVQGSRVLVD-4.77435-5.80965
HLA-B52:013W398484SDRHAVQGSRVLVD-6.80875-6.92215
HLA-B52:013W398484SDRHAVQGSRVLVD-4.20386-5.23916
HLA-A11:014UQ28484SDRHAVQGSRVLVD-7.5194-8.5547
HLA-A11:014UQ28484SDRHAVQGSRVLVD-6.9601-7.0735
HLA-A24:025HGA8484SDRHAVQGSRVLVD-7.52403-7.63743
HLA-A24:025HGA8484SDRHAVQGSRVLVD-5.82433-6.85963
HLA-B27:056PYJ8484SDRHAVQGSRVLVD-3.28285-4.31815
HLA-B44:053DX88484SDRHAVQGSRVLVD-5.91172-6.94702
HLA-B44:053DX88484SDRHAVQGSRVLVD-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of PHC3-GNA12

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
PHC3-GNA12chr3169896561chr728347771019AVQGSRVLVGCTGTACAGGGCTCAAGGGTTCTTGTT
PHC3-GNA12chr3169896561chr72834777718DRHAVQGSRVLGACCGACATGCTGTACAGGGCTCAAGGGTTCTT
PHC3-GNA12chr3169896561chr72834777817RHAVQGSRVCGACATGCTGTACAGGGCTCAAGGGTT
PHC3-GNA12chr3169896561chr72834777818RHAVQGSRVLCGACATGCTGTACAGGGCTCAAGGGTTCTT
PHC3-GNA12chr3169896561chr72834777918HAVQGSRVLCATGCTGTACAGGGCTCAAGGGTTCTT

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
PHC3-GNA12chr3169896561chr72834777015ISVYSGSDRHAVQGSATCTCTGTCTACAGTGGTTCAGACCGACATGCTGTACAGGGCTCA
PHC3-GNA12chr3169896561chr728347771025AVQGSRVLVDARDKLGCTGTACAGGGCTCAAGGGTTCTTGTTGATGCACGAGATAAGCTT
PHC3-GNA12chr3169896561chr728347771126VQGSRVLVDARDKLGGTACAGGGCTCAAGGGTTCTTGTTGATGCACGAGATAAGCTTGGC

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Information of the samples that have these potential fusion neoantigens of PHC3-GNA12

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
HNSCPHC3-GNA12chr3169896561ENST00000467570chr72834777ENST00000275364TCGA-CQ-A4CA-01A

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Potential target of CAR-T therapy development for PHC3-GNA12

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 PHC3-GNA12

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 PHC3-GNA12

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