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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:PCM1-HMBOX1 (FusionGDB2 ID:62941)

Fusion Gene Summary for PCM1-HMBOX1

check button Fusion gene summary
Fusion gene informationFusion gene name: PCM1-HMBOX1
Fusion gene ID: 62941
HgeneTgene
Gene symbol

PCM1

HMBOX1

Gene ID

5108

79618

Gene namepericentriolar material 1homeobox containing 1
SynonymsPTC4|RET/PCM-1HNF1LA|HOT1|PBHNF|TAH1
Cytomap

8p22

8p21.1-p12

Type of geneprotein-codingprotein-coding
Descriptionpericentriolar material 1 proteinPCM-1hPCM-1pericentriolar material 1, PCM1homeobox-containing protein 1homeobox telomere-binding protein 1homeobox-containing protein PBHNFtelomere-associated homeobox-containing protein 1
Modification date2020032720200313
UniProtAcc.

Q6NT76

Ensembl transtripts involved in fusion geneENST00000325083, ENST00000519253, 
ENST00000524226, ENST00000518537, 
ENST00000518936, ENST00000327578, 
ENST00000403668, ENST00000444075, 
ENST00000287701, ENST00000558662, 
ENST00000523613, ENST00000397358, 
ENST00000519047, ENST00000355231, 
ENST00000524238, ENST00000517386, 
Fusion gene scores* DoF score16 X 16 X 12=30725 X 5 X 3=75
# samples 165
** MAII scorelog2(16/3072*10)=-4.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/75*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PCM1 [Title/Abstract] AND HMBOX1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPCM1(17851128)-HMBOX1(28866588), # samples:2
Anticipated loss of major functional domain due to fusion event.PCM1-HMBOX1 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
PCM1-HMBOX1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
PCM1-HMBOX1 seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF.
PCM1-HMBOX1 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
TgeneHMBOX1

GO:0000122

negative regulation of transcription by RNA polymerase II

21839858

TgeneHMBOX1

GO:0032212

positive regulation of telomere maintenance via telomerase

23685356

TgeneHMBOX1

GO:0045892

negative regulation of transcription, DNA-templated

19757162

TgeneHMBOX1

GO:0051972

regulation of telomerase activity

23685356

TgeneHMBOX1

GO:0051973

positive regulation of telomerase activity

23685356


check buttonFusion gene breakpoints across PCM1 (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 HMBOX1 (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
ChimerDB4ESCATCGA-L5-A8NWPCM1chr8

17851128

+HMBOX1chr8

28866588

+
ChimerDB4ESCATCGA-L5-A8NWPCM1chr8

17851128

+HMBOX1chr8

28866588

+


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Fusion Gene ORF analysis for PCM1-HMBOX1

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
Frame-shiftENST00000325083ENST00000403668PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000325083ENST00000444075PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000325083ENST00000287701PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000325083ENST00000558662PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000325083ENST00000523613PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000325083ENST00000397358PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000325083ENST00000519047PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000325083ENST00000355231PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000325083ENST00000524238PCM1chr8

17851128

+HMBOX1chr8

28866588

+
5CDS-intronENST00000325083ENST00000517386PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000519253ENST00000403668PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000519253ENST00000444075PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000519253ENST00000287701PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000519253ENST00000558662PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000519253ENST00000523613PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000519253ENST00000397358PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000519253ENST00000519047PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000519253ENST00000355231PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000519253ENST00000524238PCM1chr8

17851128

+HMBOX1chr8

28866588

+
5CDS-intronENST00000519253ENST00000517386PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000524226ENST00000403668PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000524226ENST00000444075PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000524226ENST00000287701PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000524226ENST00000558662PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000524226ENST00000523613PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000524226ENST00000397358PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000524226ENST00000519047PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000524226ENST00000355231PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000524226ENST00000524238PCM1chr8

17851128

+HMBOX1chr8

28866588

+
5CDS-intronENST00000524226ENST00000517386PCM1chr8

17851128

+HMBOX1chr8

28866588

+
intron-3CDSENST00000518537ENST00000403668PCM1chr8

17851128

+HMBOX1chr8

28866588

+
intron-3CDSENST00000518537ENST00000444075PCM1chr8

17851128

+HMBOX1chr8

28866588

+
intron-3CDSENST00000518537ENST00000287701PCM1chr8

17851128

+HMBOX1chr8

28866588

+
intron-3CDSENST00000518537ENST00000558662PCM1chr8

17851128

+HMBOX1chr8

28866588

+
intron-3CDSENST00000518537ENST00000523613PCM1chr8

17851128

+HMBOX1chr8

28866588

+
intron-3CDSENST00000518537ENST00000397358PCM1chr8

17851128

+HMBOX1chr8

28866588

+
intron-3CDSENST00000518537ENST00000519047PCM1chr8

17851128

+HMBOX1chr8

28866588

+
intron-3CDSENST00000518537ENST00000355231PCM1chr8

17851128

+HMBOX1chr8

28866588

+
intron-3CDSENST00000518537ENST00000524238PCM1chr8

17851128

+HMBOX1chr8

28866588

+
intron-intronENST00000518537ENST00000517386PCM1chr8

17851128

+HMBOX1chr8

28866588

+
intron-3CDSENST00000518936ENST00000403668PCM1chr8

17851128

+HMBOX1chr8

28866588

+
intron-3CDSENST00000518936ENST00000444075PCM1chr8

17851128

+HMBOX1chr8

28866588

+
intron-3CDSENST00000518936ENST00000287701PCM1chr8

17851128

+HMBOX1chr8

28866588

+
intron-3CDSENST00000518936ENST00000558662PCM1chr8

17851128

+HMBOX1chr8

28866588

+
intron-3CDSENST00000518936ENST00000523613PCM1chr8

17851128

+HMBOX1chr8

28866588

+
intron-3CDSENST00000518936ENST00000397358PCM1chr8

17851128

+HMBOX1chr8

28866588

+
intron-3CDSENST00000518936ENST00000519047PCM1chr8

17851128

+HMBOX1chr8

28866588

+
intron-3CDSENST00000518936ENST00000355231PCM1chr8

17851128

+HMBOX1chr8

28866588

+
intron-3CDSENST00000518936ENST00000524238PCM1chr8

17851128

+HMBOX1chr8

28866588

+
intron-intronENST00000518936ENST00000517386PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000327578ENST00000403668PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000327578ENST00000444075PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000327578ENST00000287701PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000327578ENST00000558662PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000327578ENST00000523613PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000327578ENST00000397358PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000327578ENST00000519047PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000327578ENST00000355231PCM1chr8

17851128

+HMBOX1chr8

28866588

+
Frame-shiftENST00000327578ENST00000524238PCM1chr8

17851128

+HMBOX1chr8

28866588

+
5CDS-intronENST00000327578ENST00000517386PCM1chr8

17851128

+HMBOX1chr8

28866588

+

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)

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

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Fusion Genomic Features for PCM1-HMBOX1


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)
PCM1chr817851128+HMBOX1chr828866588+0.0012129450.9987871
PCM1chr817851128+HMBOX1chr828866588+0.0012129450.9987871

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 PCM1-HMBOX1


check button Go to

FGviewer for the breakpoints of :-:

.
- 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
.HMBOX1

Q6NT76

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: Binds directly to 5'-TTAGGG-3' repeats in telomeric DNA (PubMed:23813958, PubMed:23685356). Associates with the telomerase complex at sites of active telomere processing and positively regulates telomere elongation (PubMed:23685356). Important for TERT binding to chromatin, indicating a role in recruitment of the telomerase complex to telomeres (By similarity). Also plays a role in the alternative lengthening of telomeres (ALT) pathway in telomerase-negative cells where it promotes formation and/or maintenance of ALT-associated promyelocytic leukemia bodies (APBs) (PubMed:23813958). Enhances formation of telomere C-circles in ALT cells, suggesting a possible role in telomere recombination (PubMed:23813958). Might also be involved in the DNA damage response at telomeres (PubMed:23813958). {ECO:0000250|UniProtKB:Q8BJA3, ECO:0000269|PubMed:23685356, ECO:0000269|PubMed:23813958}.

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


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Fusion Gene Sequence for PCM1-HMBOX1


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.

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Fusion Gene PPI Analysis for PCM1-HMBOX1


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 PCM1-HMBOX1


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 PCM1-HMBOX1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePCM1C0036341Schizophrenia1CTD_human
HgenePCM1C0238463Papillary thyroid carcinoma1ORPHANET