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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:PHC3-SEC62

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PHC3-SEC62
FusionPDB ID: 64751
FusionGDB2.0 ID: 64751
HgeneTgene
Gene symbol

PHC3

SEC62

Gene ID

80012

7095

Gene namepolyhomeotic homolog 3SEC62 homolog, preprotein translocation factor
SynonymsEDR3|HPH3Dtrp1|HTP1|TLOC1|TP-1
Cytomap

3q26.2

3q26.2

Type of geneprotein-codingprotein-coding
Descriptionpolyhomeotic-like protein 3early development regulator 3early development regulatory protein 3homolog of polyhomeotic 3polyhomeotic like 3translocation protein SEC62SEC62 preprotein translocation factorhTP-1membrane protein SEC62, S.cerevisiae, homolog oftranslocation protein 1
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST idsENST00000467570, ENST00000494943, 
ENST00000495893, ENST00000474275, 
ENST00000481639, ENST00000497658, 
ENST00000470355, ENST00000337002, 
ENST00000480708, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score15 X 15 X 11=247517 X 20 X 8=2720
# samples 2025
** MAII scorelog2(20/2475*10)=-3.62935662007961
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(25/2720*10)=-3.44360665147561
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: PHC3 [Title/Abstract] AND SEC62 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PHC3(169854207)-SEC62(169710382), # samples:1
SEC62(169703653)-PHC3(169840532), # samples:1
Anticipated loss of major functional domain due to fusion event.PHC3-SEC62 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-SEC62 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-SEC62 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-SEC62 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-SEC62 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
PHC3-SEC62 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
PHC3-SEC62 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
PHC3-SEC62 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
SEC62-PHC3 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
SEC62-PHC3 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF.
SEC62-PHC3 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
SEC62-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 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 SEC62 (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 Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4BRCATCGA-A8-A09Z-01APHC3chr3

169854207

-SEC62chr3

169710382

+


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Fusion ORF Analysis


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)
ENST00000495893PHC3chr3169854207-ENST00000480708SEC62chr3169710382+1636951321420462
ENST00000494943PHC3chr3169854207-ENST00000480708SEC62chr3169710382+1637952691421450
ENST00000467570PHC3chr3169854207-ENST00000480708SEC62chr3169710382+1479794341263409

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
ENST00000495893ENST00000480708PHC3chr3169854207-SEC62chr3169710382+0.0122513580.98774856
ENST00000494943ENST00000480708PHC3chr3169854207-SEC62chr3169710382+0.0169391860.9830608
ENST00000467570ENST00000480708PHC3chr3169854207-SEC62chr3169710382+0.007773920.9922261

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>64751_64751_1_PHC3-SEC62_PHC3_chr3_169854207_ENST00000467570_SEC62_chr3_169710382_ENST00000480708_length(amino acids)=409AA_BP=3
MAEAEFKDHSTAMDTEPNPGTSSVSTTTSSTTTTTITTSSSRMQQPQISVYSGSDRHAVQVIQQALHRPPSSAAQYLQQMYAAQQQHLML
HTAALQQQHLSSSQLQSLAAVQASLSSGRPSTSPTGSVTQQSSMSQTSLIFTPATTVAAVQSDIPVVSSSSSSSCQSAATQVQNLTLRSQ
KLGVLSSSQNGPPKSTSQTQSLTICHNKTTVTSSKISQRDPSPESNKKGESPSLESRSTAVTRTSSIHQLIAPARCILFLIIWLITGGRH
HFWFLPNLTADVGFIDSFRPLYTHEYKGPKADLKKDEKSETKKQQKSDSEEKSDSEKKEDEEGKVGPGNHGTEGSGGERHSDTDSDRRED

--------------------------------------------------------------

>64751_64751_2_PHC3-SEC62_PHC3_chr3_169854207_ENST00000494943_SEC62_chr3_169710382_ENST00000480708_length(amino acids)=450AA_BP=0
MDTEPNPGTSSVSTTTSSTTTTTITTSSSRMQQPQISVYSGSDRHAVQVIQQALHRPPSSAAQYLQQMYAAQQQHLMLHTAALQQQHLSS
SQLQSLAAVQASLSSGRPSTSPTGSVTQQSSMSQTSINLSTSPTPAQLISRSQASSSTSGSITQQTMLLGSTSPTLTASQAQMYLRAQML
IFTPATTVAAVQSDIPVVSSSSSSSCQSAATQVQNLTLRSQKLGVLSSSQNGPPKSTSQTQSLTICHNKTTVTSSKISQRDPSPESNKKG
ESPSLESRSTAVTRTSSIHQLIAPARCILFLIIWLITGGRHHFWFLPNLTADVGFIDSFRPLYTHEYKGPKADLKKDEKSETKKQQKSDS
EEKSDSEKKEDEEGKVGPGNHGTEGSGGERHSDTDSDRREDDRSQHSSGNGNDFEMITKEELEQQTDGDCEEDEEEENDGETPKSSHEKS

--------------------------------------------------------------

>64751_64751_3_PHC3-SEC62_PHC3_chr3_169854207_ENST00000495893_SEC62_chr3_169710382_ENST00000480708_length(amino acids)=462AA_BP=3
MAEAEFKDHSTAMDTEPNPGTSSVSTTTSSTTTTTITTSSSRMQQPQISVYSGSDRHAVQVIQQALHRPPSSAAQYLQQMYAAQQQHLML
HTAALQQQHLSSSQLQSLAAVQASLSSGRPSTSPTGSVTQQSSMSQTSINLSTSPTPAQLISRSQASSSTSGSITQQTMLLGSTSPTLTA
SQAQMYLRAQMLIFTPATTVAAVQSDIPVVSSSSSSSCQSAATQVQNLTLRSQKLGVLSSSQNGPPKSTSQTQSLTICHNKTTVTSSKIS
QRDPSPESNKKGESPSLESRSTAVTRTSSIHQLIAPARCILFLIIWLITGGRHHFWFLPNLTADVGFIDSFRPLYTHEYKGPKADLKKDE
KSETKKQQKSDSEEKSDSEKKEDEEGKVGPGNHGTEGSGGERHSDTDSDRREDDRSQHSSGNGNDFEMITKEELEQQTDGDCEEDEEEEN

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Fusion Protein Functional Features


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/chr3:169854207/chr3:169710382)
- 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 buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
..
FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePHC3chr3:169854207chr3:169710382ENST00000494943-71519_26294.3333333333333984.0Compositional biasNote=Poly-Thr
HgenePHC3chr3:169854207chr3:169710382ENST00000494943-71589_287294.3333333333333984.0Compositional biasNote=Ser-rich
HgenePHC3chr3:169854207chr3:169710382ENST00000495893-71519_26306.3333333333333996.0Compositional biasNote=Poly-Thr
HgenePHC3chr3:169854207chr3:169710382ENST00000495893-71589_287306.3333333333333996.0Compositional biasNote=Ser-rich
TgeneSEC62chr3:169854207chr3:169710382ENST0000033700268256_399243.33333333333334400.0Topological domainCytoplasmic
TgeneSEC62chr3:169854207chr3:169710382ENST0000048070869256_399243.33333333333334442.0Topological domainCytoplasmic

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePHC3chr3:169854207chr3:169710382ENST00000474275-1519_260187.0Compositional biasNote=Poly-Thr
HgenePHC3chr3:169854207chr3:169710382ENST00000474275-15324_5390187.0Compositional biasNote=Gln-rich
HgenePHC3chr3:169854207chr3:169710382ENST00000474275-15346_6700187.0Compositional biasNote=Pro-rich
HgenePHC3chr3:169854207chr3:169710382ENST00000474275-1589_2870187.0Compositional biasNote=Ser-rich
HgenePHC3chr3:169854207chr3:169710382ENST00000494943-715324_539294.3333333333333984.0Compositional biasNote=Gln-rich
HgenePHC3chr3:169854207chr3:169710382ENST00000494943-715346_670294.3333333333333984.0Compositional biasNote=Pro-rich
HgenePHC3chr3:169854207chr3:169710382ENST00000495893-715324_539306.3333333333333996.0Compositional biasNote=Gln-rich
HgenePHC3chr3:169854207chr3:169710382ENST00000495893-715346_670306.3333333333333996.0Compositional biasNote=Pro-rich
HgenePHC3chr3:169854207chr3:169710382ENST00000497658-1419_260152.0Compositional biasNote=Poly-Thr
HgenePHC3chr3:169854207chr3:169710382ENST00000497658-14324_5390152.0Compositional biasNote=Gln-rich
HgenePHC3chr3:169854207chr3:169710382ENST00000497658-14346_6700152.0Compositional biasNote=Pro-rich
HgenePHC3chr3:169854207chr3:169710382ENST00000497658-1489_2870152.0Compositional biasNote=Ser-rich
HgenePHC3chr3:169854207chr3:169710382ENST00000474275-15919_9830187.0DomainSAM
HgenePHC3chr3:169854207chr3:169710382ENST00000494943-715919_983294.3333333333333984.0DomainSAM
HgenePHC3chr3:169854207chr3:169710382ENST00000495893-715919_983306.3333333333333996.0DomainSAM
HgenePHC3chr3:169854207chr3:169710382ENST00000497658-14919_9830152.0DomainSAM
HgenePHC3chr3:169854207chr3:169710382ENST00000474275-15691_7200187.0MotifNote=HD1
HgenePHC3chr3:169854207chr3:169710382ENST00000494943-715691_720294.3333333333333984.0MotifNote=HD1
HgenePHC3chr3:169854207chr3:169710382ENST00000495893-715691_720306.3333333333333996.0MotifNote=HD1
HgenePHC3chr3:169854207chr3:169710382ENST00000497658-14691_7200152.0MotifNote=HD1
HgenePHC3chr3:169854207chr3:169710382ENST00000474275-15776_8100187.0Zinc fingerFCS-type
HgenePHC3chr3:169854207chr3:169710382ENST00000494943-715776_810294.3333333333333984.0Zinc fingerFCS-type
HgenePHC3chr3:169854207chr3:169710382ENST00000495893-715776_810306.3333333333333996.0Zinc fingerFCS-type
HgenePHC3chr3:169854207chr3:169710382ENST00000497658-14776_8100152.0Zinc fingerFCS-type
TgeneSEC62chr3:169854207chr3:169710382ENST00000337002681_196243.33333333333334400.0Topological domainCytoplasmic
TgeneSEC62chr3:169854207chr3:169710382ENST0000033700268218_234243.33333333333334400.0Topological domainLumenal
TgeneSEC62chr3:169854207chr3:169710382ENST00000480708691_196243.33333333333334442.0Topological domainCytoplasmic
TgeneSEC62chr3:169854207chr3:169710382ENST0000048070869218_234243.33333333333334442.0Topological domainLumenal
TgeneSEC62chr3:169854207chr3:169710382ENST0000033700268197_217243.33333333333334400.0TransmembraneHelical
TgeneSEC62chr3:169854207chr3:169710382ENST0000033700268235_255243.33333333333334400.0TransmembraneHelical
TgeneSEC62chr3:169854207chr3:169710382ENST0000048070869197_217243.33333333333334442.0TransmembraneHelical
TgeneSEC62chr3:169854207chr3:169710382ENST0000048070869235_255243.33333333333334442.0TransmembraneHelical


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
PHC3
SEC62


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to PHC3-SEC62


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-SEC62


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