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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:TPD52-PHGDH (FusionGDB2 ID:92649)

Fusion Gene Summary for TPD52-PHGDH

check button Fusion gene summary
Fusion gene informationFusion gene name: TPD52-PHGDH
Fusion gene ID: 92649
HgeneTgene
Gene symbol

TPD52

PHGDH

Gene ID

7163

26227

Gene nametumor protein D52phosphoglycerate dehydrogenase
SynonymsD52|N8L|PC-1|PrLZ|hD523-PGDH|3PGDH|HEL-S-113|NLS|NLS1|PDG|PGAD|PGD|PGDH|PHGDHD|SERA
Cytomap

8q21.13

1p12

Type of geneprotein-codingprotein-coding
Descriptiontumor protein D52prostate and colon associated proteinprostate leucine zipperprotein N8D-3-phosphoglycerate dehydrogenase2-oxoglutarate reductase3-phosphoglycerate dehydrogenaseepididymis secretory protein Li 113malate dehydrogenase
Modification date2020031320200320
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000537855, ENST00000379096, 
ENST00000518937, ENST00000519303, 
ENST00000517427, ENST00000520527, 
ENST00000448733, ENST00000379097, 
ENST00000523395, 		ENST00000369409, 
ENST00000369407, ENST00000482968, 
Fusion gene scores* DoF score21 X 15 X 9=283515 X 10 X 8=1200
# samples 3016
** MAII scorelog2(30/2835*10)=-3.24031432933371
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(16/1200*10)=-2.90689059560852
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TPD52 [Title/Abstract] AND PHGDH [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTPD52(81083660)-PHGDH(120285430), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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 TPD52 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across PHGDH (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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
ChimerDB4BLCATCGA-FD-A5BV-01ATPD52chr8

81083660

-PHGDHchr1

120285430

+


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Fusion Gene ORF analysis for TPD52-PHGDH

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
intron-3CDSENST00000537855ENST00000369409TPD52chr8

81083660

-PHGDHchr1

120285430

+
intron-3CDSENST00000537855ENST00000369407TPD52chr8

81083660

-PHGDHchr1

120285430

+
intron-3UTRENST00000537855ENST00000482968TPD52chr8

81083660

-PHGDHchr1

120285430

+
In-frameENST00000379096ENST00000369409TPD52chr8

81083660

-PHGDHchr1

120285430

+
In-frameENST00000379096ENST00000369407TPD52chr8

81083660

-PHGDHchr1

120285430

+
5CDS-3UTRENST00000379096ENST00000482968TPD52chr8

81083660

-PHGDHchr1

120285430

+
In-frameENST00000518937ENST00000369409TPD52chr8

81083660

-PHGDHchr1

120285430

+
In-frameENST00000518937ENST00000369407TPD52chr8

81083660

-PHGDHchr1

120285430

+
5CDS-3UTRENST00000518937ENST00000482968TPD52chr8

81083660

-PHGDHchr1

120285430

+
intron-3CDSENST00000519303ENST00000369409TPD52chr8

81083660

-PHGDHchr1

120285430

+
intron-3CDSENST00000519303ENST00000369407TPD52chr8

81083660

-PHGDHchr1

120285430

+
intron-3UTRENST00000519303ENST00000482968TPD52chr8

81083660

-PHGDHchr1

120285430

+
intron-3CDSENST00000517427ENST00000369409TPD52chr8

81083660

-PHGDHchr1

120285430

+
intron-3CDSENST00000517427ENST00000369407TPD52chr8

81083660

-PHGDHchr1

120285430

+
intron-3UTRENST00000517427ENST00000482968TPD52chr8

81083660

-PHGDHchr1

120285430

+
intron-3CDSENST00000520527ENST00000369409TPD52chr8

81083660

-PHGDHchr1

120285430

+
intron-3CDSENST00000520527ENST00000369407TPD52chr8

81083660

-PHGDHchr1

120285430

+
intron-3UTRENST00000520527ENST00000482968TPD52chr8

81083660

-PHGDHchr1

120285430

+
intron-3CDSENST00000448733ENST00000369409TPD52chr8

81083660

-PHGDHchr1

120285430

+
intron-3CDSENST00000448733ENST00000369407TPD52chr8

81083660

-PHGDHchr1

120285430

+
intron-3UTRENST00000448733ENST00000482968TPD52chr8

81083660

-PHGDHchr1

120285430

+
intron-3CDSENST00000379097ENST00000369409TPD52chr8

81083660

-PHGDHchr1

120285430

+
intron-3CDSENST00000379097ENST00000369407TPD52chr8

81083660

-PHGDHchr1

120285430

+
intron-3UTRENST00000379097ENST00000482968TPD52chr8

81083660

-PHGDHchr1

120285430

+
intron-3CDSENST00000523395ENST00000369409TPD52chr8

81083660

-PHGDHchr1

120285430

+
intron-3CDSENST00000523395ENST00000369407TPD52chr8

81083660

-PHGDHchr1

120285430

+
intron-3UTRENST00000523395ENST00000482968TPD52chr8

81083660

-PHGDHchr1

120285430

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000379096TPD52chr881083660-ENST00000369409PHGDHchr1120285430+70213432526164
ENST00000379096TPD52chr881083660-ENST00000369407PHGDHchr1120285430+70013432526164
ENST00000518937TPD52chr881083660-ENST00000369409PHGDHchr1120285430+803235133627164
ENST00000518937TPD52chr881083660-ENST00000369407PHGDHchr1120285430+801235133627164

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
ENST00000379096ENST00000369409TPD52chr881083660-PHGDHchr1120285430+0.56447460.4355254
ENST00000379096ENST00000369407TPD52chr881083660-PHGDHchr1120285430+0.543456440.45654356
ENST00000518937ENST00000369409TPD52chr881083660-PHGDHchr1120285430+0.626553650.37344635
ENST00000518937ENST00000369407TPD52chr881083660-PHGDHchr1120285430+0.60444460.39555535

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Fusion Genomic Features for TPD52-PHGDH


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)
TPD52chr881083659-PHGDHchr1120285429+0.0002337160.9997663
TPD52chr881083659-PHGDHchr1120285429+0.0002337160.9997663

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for TPD52-PHGDH


check button Go to

FGviewer for the breakpoints of chr8:81083660-chr1:120285430

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
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.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneTPD52chr8:81083660chr1:120285430ENST00000379096-1662_1146.333333333333333185.0Coiled coilOntology_term=ECO:0000255
HgeneTPD52chr8:81083660chr1:120285430ENST00000379097-1662_1140225.0Coiled coilOntology_term=ECO:0000255
HgeneTPD52chr8:81083660chr1:120285430ENST00000448733-1762_1140239.0Coiled coilOntology_term=ECO:0000255
HgeneTPD52chr8:81083660chr1:120285430ENST00000517427-1762_1140234.0Coiled coilOntology_term=ECO:0000255
HgeneTPD52chr8:81083660chr1:120285430ENST00000518937-1862_1146.333333333333333208.0Coiled coilOntology_term=ECO:0000255
HgeneTPD52chr8:81083660chr1:120285430ENST00000520527-1862_1140248.0Coiled coilOntology_term=ECO:0000255
TgenePHGDHchr8:81083660chr1:120285430ENST00000369409912155_156403.0534.0Nucleotide bindingNAD
TgenePHGDHchr8:81083660chr1:120285430ENST00000369409912234_236403.0534.0Nucleotide bindingNAD
TgenePHGDHchr8:81083660chr1:120285430ENST00000369409912283_286403.0534.0Nucleotide bindingNAD


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Fusion Gene Sequence for TPD52-PHGDH


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>In-frame_ENST00000379096_ENST00000369409_TCGA-FD-A5BV-01A_TPD52_chr8_81083660_-_PHGDH_chr1_120285430_length(transcript)=702nt_BP=134nt
GCGGGAGTCGCCGGCGGAGGCGAGGAGGAGCTCTGCGCGGCGCGGCGGGCGATCCGAGCCGGGACGGGCTGCAGGCGGGGGTGCTGCAGA
GGACACGAGGCGGCGGGCTGGAGACATGGACCGCGGCGAGCAAGGTCACCACCTCCCACAGCCCTGCTGCACCAGGGGAGCAAGGCTTCG
GGGAATGCCTCCTGGCCGTGGCCCTGGCAGGCGCCCCTTACCAGGCTGTGGGCTTGGTCCAAGGCACTACGCCTGTACTGCAGGGGCTCA
ATGGAGCTGTCTTCAGGCCAGAAGTGCCTCTCCGCAGGGACCTGCCCCTGCTCCTATTCCGGACTCAGACCTCTGACCCTGCAATGCTGC
CTACCATGATTGGCCTCCTGGCAGAGGCAGGCGTGCGGCTGCTGTCCTACCAGACTTCACTGGTGTCAGATGGGGAGACCTGGCACGTCA
TGGGCATCTCCTCCTTGCTGCCCAGCCTGGAAGCGTGGAAGCAGCATGTGACTGAAGCCTTCCAGTTCCACTTCTAACCTTGGAGCTCAC
TGGTCCCTGCCTCTGGGGCTTTTCTGAAGAAACCCACCCACTGTGATCAATAGGGAGAGAAAATCCACATTCTTGGGCTGAACGCGGGCC

>In-frame_ENST00000379096_ENST00000369409_TCGA-FD-A5BV-01A_TPD52_chr8_81083660_-_PHGDH_chr1_120285430_length(amino acids)=164AA_start in transcript=32_stop in transcript=526
MRGAAGDPSRDGLQAGVLQRTRGGGLETWTAASKVTTSHSPAAPGEQGFGECLLAVALAGAPYQAVGLVQGTTPVLQGLNGAVFRPEVPL

--------------------------------------------------------------
>In-frame_ENST00000379096_ENST00000369407_TCGA-FD-A5BV-01A_TPD52_chr8_81083660_-_PHGDH_chr1_120285430_length(transcript)=700nt_BP=134nt
GCGGGAGTCGCCGGCGGAGGCGAGGAGGAGCTCTGCGCGGCGCGGCGGGCGATCCGAGCCGGGACGGGCTGCAGGCGGGGGTGCTGCAGA
GGACACGAGGCGGCGGGCTGGAGACATGGACCGCGGCGAGCAAGGTCACCACCTCCCACAGCCCTGCTGCACCAGGGGAGCAAGGCTTCG
GGGAATGCCTCCTGGCCGTGGCCCTGGCAGGCGCCCCTTACCAGGCTGTGGGCTTGGTCCAAGGCACTACGCCTGTACTGCAGGGGCTCA
ATGGAGCTGTCTTCAGGCCAGAAGTGCCTCTCCGCAGGGACCTGCCCCTGCTCCTATTCCGGACTCAGACCTCTGACCCTGCAATGCTGC
CTACCATGATTGGCCTCCTGGCAGAGGCAGGCGTGCGGCTGCTGTCCTACCAGACTTCACTGGTGTCAGATGGGGAGACCTGGCACGTCA
TGGGCATCTCCTCCTTGCTGCCCAGCCTGGAAGCGTGGAAGCAGCATGTGACTGAAGCCTTCCAGTTCCACTTCTAACCTTGGAGCTCAC
TGGTCCCTGCCTCTGGGGCTTTTCTGAAGAAACCCACCCACTGTGATCAATAGGGAGAGAAAATCCACATTCTTGGGCTGAACGCGGGCC

>In-frame_ENST00000379096_ENST00000369407_TCGA-FD-A5BV-01A_TPD52_chr8_81083660_-_PHGDH_chr1_120285430_length(amino acids)=164AA_start in transcript=32_stop in transcript=526
MRGAAGDPSRDGLQAGVLQRTRGGGLETWTAASKVTTSHSPAAPGEQGFGECLLAVALAGAPYQAVGLVQGTTPVLQGLNGAVFRPEVPL

--------------------------------------------------------------
>In-frame_ENST00000518937_ENST00000369409_TCGA-FD-A5BV-01A_TPD52_chr8_81083660_-_PHGDH_chr1_120285430_length(transcript)=803nt_BP=235nt
AGGTCGACCGGGTCAGGTGGTTGGGTGACGCCCCAGGAAAGCGCTCCAGGCCGAGGGCGGGCGGCGCCGCCGCGCCCGACGCCTCTGGGG
GTGGGGACTTCGCGGGAGTCGCCGGCGGAGGCGAGGAGGAGCTCTGCGCGGCGCGGCGGGCGATCCGAGCCGGGACGGGCTGCAGGCGGG
GGTGCTGCAGAGGACACGAGGCGGCGGGCTGGAGACATGGACCGCGGCGAGCAAGGTCACCACCTCCCACAGCCCTGCTGCACCAGGGGA
GCAAGGCTTCGGGGAATGCCTCCTGGCCGTGGCCCTGGCAGGCGCCCCTTACCAGGCTGTGGGCTTGGTCCAAGGCACTACGCCTGTACT
GCAGGGGCTCAATGGAGCTGTCTTCAGGCCAGAAGTGCCTCTCCGCAGGGACCTGCCCCTGCTCCTATTCCGGACTCAGACCTCTGACCC
TGCAATGCTGCCTACCATGATTGGCCTCCTGGCAGAGGCAGGCGTGCGGCTGCTGTCCTACCAGACTTCACTGGTGTCAGATGGGGAGAC
CTGGCACGTCATGGGCATCTCCTCCTTGCTGCCCAGCCTGGAAGCGTGGAAGCAGCATGTGACTGAAGCCTTCCAGTTCCACTTCTAACC
TTGGAGCTCACTGGTCCCTGCCTCTGGGGCTTTTCTGAAGAAACCCACCCACTGTGATCAATAGGGAGAGAAAATCCACATTCTTGGGCT

>In-frame_ENST00000518937_ENST00000369409_TCGA-FD-A5BV-01A_TPD52_chr8_81083660_-_PHGDH_chr1_120285430_length(amino acids)=164AA_start in transcript=133_stop in transcript=627
MRGAAGDPSRDGLQAGVLQRTRGGGLETWTAASKVTTSHSPAAPGEQGFGECLLAVALAGAPYQAVGLVQGTTPVLQGLNGAVFRPEVPL

--------------------------------------------------------------
>In-frame_ENST00000518937_ENST00000369407_TCGA-FD-A5BV-01A_TPD52_chr8_81083660_-_PHGDH_chr1_120285430_length(transcript)=801nt_BP=235nt
AGGTCGACCGGGTCAGGTGGTTGGGTGACGCCCCAGGAAAGCGCTCCAGGCCGAGGGCGGGCGGCGCCGCCGCGCCCGACGCCTCTGGGG
GTGGGGACTTCGCGGGAGTCGCCGGCGGAGGCGAGGAGGAGCTCTGCGCGGCGCGGCGGGCGATCCGAGCCGGGACGGGCTGCAGGCGGG
GGTGCTGCAGAGGACACGAGGCGGCGGGCTGGAGACATGGACCGCGGCGAGCAAGGTCACCACCTCCCACAGCCCTGCTGCACCAGGGGA
GCAAGGCTTCGGGGAATGCCTCCTGGCCGTGGCCCTGGCAGGCGCCCCTTACCAGGCTGTGGGCTTGGTCCAAGGCACTACGCCTGTACT
GCAGGGGCTCAATGGAGCTGTCTTCAGGCCAGAAGTGCCTCTCCGCAGGGACCTGCCCCTGCTCCTATTCCGGACTCAGACCTCTGACCC
TGCAATGCTGCCTACCATGATTGGCCTCCTGGCAGAGGCAGGCGTGCGGCTGCTGTCCTACCAGACTTCACTGGTGTCAGATGGGGAGAC
CTGGCACGTCATGGGCATCTCCTCCTTGCTGCCCAGCCTGGAAGCGTGGAAGCAGCATGTGACTGAAGCCTTCCAGTTCCACTTCTAACC
TTGGAGCTCACTGGTCCCTGCCTCTGGGGCTTTTCTGAAGAAACCCACCCACTGTGATCAATAGGGAGAGAAAATCCACATTCTTGGGCT

>In-frame_ENST00000518937_ENST00000369407_TCGA-FD-A5BV-01A_TPD52_chr8_81083660_-_PHGDH_chr1_120285430_length(amino acids)=164AA_start in transcript=133_stop in transcript=627
MRGAAGDPSRDGLQAGVLQRTRGGGLETWTAASKVTTSHSPAAPGEQGFGECLLAVALAGAPYQAVGLVQGTTPVLQGLNGAVFRPEVPL

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

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Fusion Gene PPI Analysis for TPD52-PHGDH


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 (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for TPD52-PHGDH


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for TPD52-PHGDH


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneTPD52C0033578Prostatic Neoplasms2CTD_human
HgeneTPD52C0376358Malignant neoplasm of prostate2CTD_human
HgeneTPD52C0027643Neoplasm Recurrence, Local1CTD_human
TgenePHGDHC1866174Phosphoglycerate Dehydrogenase Deficiency4CTD_human;GENOMICS_ENGLAND;UNIPROT
TgenePHGDHC4551478NEU-LAXOVA SYNDROME 14GENOMICS_ENGLAND;UNIPROT
TgenePHGDHC0006142Malignant neoplasm of breast1CTD_human
TgenePHGDHC0007131Non-Small Cell Lung Carcinoma1CTD_human
TgenePHGDHC0007621Neoplastic Cell Transformation1CTD_human
TgenePHGDHC0023903Liver neoplasms1CTD_human
TgenePHGDHC0025202melanoma1CTD_human
TgenePHGDHC0033578Prostatic Neoplasms1CTD_human
TgenePHGDHC0265218Neu-Laxova syndrome1CTD_human;GENOMICS_ENGLAND;ORPHANET
TgenePHGDHC0345904Malignant neoplasm of liver1CTD_human
TgenePHGDHC0376358Malignant neoplasm of prostate1CTD_human
TgenePHGDHC05801903-Phosphoglycerate dehydrogenase deficiency1ORPHANET
TgenePHGDHC0678222Breast Carcinoma1CTD_human
TgenePHGDHC1257931Mammary Neoplasms, Human1CTD_human
TgenePHGDHC1458155Mammary Neoplasms1CTD_human
TgenePHGDHC4704874Mammary Carcinoma, Human1CTD_human