FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact
Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:CLTC-PTRH2 (FusionGDB2 ID:17420)

Fusion Gene Summary for CLTC-PTRH2

check button Fusion gene summary
Fusion gene informationFusion gene name: CLTC-PTRH2
Fusion gene ID: 17420
HgeneTgene
Gene symbol

CLTC

PTRH2

Gene ID

1213

51651

Gene nameclathrin heavy chainpeptidyl-tRNA hydrolase 2
SynonymsCHC|CHC17|CLH-17|CLTCL2|Hc|MRD56BIT1|CFAP37|CGI-147|IMNEPD|PTH|PTH 2|PTH2
Cytomap

17q23.1

17q23.1

Type of geneprotein-codingprotein-coding
Descriptionclathrin heavy chain 1clathrin heavy chain on chromosome 17clathrin, heavy polypeptide (Hc)clathrin, heavy polypeptide-like 2peptidyl-tRNA hydrolase 2, mitochondrialbcl-2 inhibitor of transcription 1cilia and flagella associated protein 37
Modification date2020031320200313
UniProtAcc

Q00610

.
Ensembl transtripts involved in fusion geneENST00000393043, ENST00000269122, 
ENST00000579456, ENST00000579815, 
ENST00000393038, ENST00000537860, 
ENST00000409433, ENST00000470557, 
ENST00000579915, 
Fusion gene scores* DoF score27 X 40 X 17=183609 X 6 X 6=324
# samples 8412
** MAII scorelog2(84/18360*10)=-4.45003292063505
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(12/324*10)=-1.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CLTC [Title/Abstract] AND PTRH2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPTRH2(57784731)-CLTC(57751007), # samples:2
CLTC(57697534)-PTRH2(57775339), # samples:1
Anticipated loss of major functional domain due to fusion event.CLTC-PTRH2 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
CLTC-PTRH2 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CLTC-PTRH2 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
HgeneCLTC

GO:1900126

negative regulation of hyaluronan biosynthetic process

24251095


check buttonFusion gene breakpoints across CLTC (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 PTRH2 (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
ChimerDB4LUADTCGA-69-7765-01ACLTCchr17

57697534

-PTRH2chr17

57775339

-


Top

Fusion Gene ORF analysis for CLTC-PTRH2

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-shiftENST00000393043ENST00000393038CLTCchr17

57697534

-PTRH2chr17

57775339

-
Frame-shiftENST00000393043ENST00000537860CLTCchr17

57697534

-PTRH2chr17

57775339

-
In-frameENST00000393043ENST00000409433CLTCchr17

57697534

-PTRH2chr17

57775339

-
In-frameENST00000393043ENST00000470557CLTCchr17

57697534

-PTRH2chr17

57775339

-
5CDS-intronENST00000393043ENST00000579915CLTCchr17

57697534

-PTRH2chr17

57775339

-
Frame-shiftENST00000269122ENST00000393038CLTCchr17

57697534

-PTRH2chr17

57775339

-
Frame-shiftENST00000269122ENST00000537860CLTCchr17

57697534

-PTRH2chr17

57775339

-
In-frameENST00000269122ENST00000409433CLTCchr17

57697534

-PTRH2chr17

57775339

-
In-frameENST00000269122ENST00000470557CLTCchr17

57697534

-PTRH2chr17

57775339

-
5CDS-intronENST00000269122ENST00000579915CLTCchr17

57697534

-PTRH2chr17

57775339

-
Frame-shiftENST00000579456ENST00000393038CLTCchr17

57697534

-PTRH2chr17

57775339

-
Frame-shiftENST00000579456ENST00000537860CLTCchr17

57697534

-PTRH2chr17

57775339

-
In-frameENST00000579456ENST00000409433CLTCchr17

57697534

-PTRH2chr17

57775339

-
In-frameENST00000579456ENST00000470557CLTCchr17

57697534

-PTRH2chr17

57775339

-
5CDS-intronENST00000579456ENST00000579915CLTCchr17

57697534

-PTRH2chr17

57775339

-
intron-3CDSENST00000579815ENST00000393038CLTCchr17

57697534

-PTRH2chr17

57775339

-
intron-3CDSENST00000579815ENST00000537860CLTCchr17

57697534

-PTRH2chr17

57775339

-
intron-3CDSENST00000579815ENST00000409433CLTCchr17

57697534

-PTRH2chr17

57775339

-
intron-3CDSENST00000579815ENST00000470557CLTCchr17

57697534

-PTRH2chr17

57775339

-
intron-intronENST00000579815ENST00000579915CLTCchr17

57697534

-PTRH2chr17

57775339

-

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

Top

Fusion Genomic Features for CLTC-PTRH2


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)

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.

Top

Fusion Protein Features for CLTC-PTRH2


check button Go to

FGviewer for the breakpoints of chr17:57697534-chr17:57775339

.
- 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
CLTC

Q00610

.
FUNCTION: Clathrin is the major protein of the polyhedral coat of coated pits and vesicles. Two different adapter protein complexes link the clathrin lattice either to the plasma membrane or to the trans-Golgi network. Acts as component of the TACC3/ch-TOG/clathrin complex proposed to contribute to stabilization of kinetochore fibers of the mitotic spindle by acting as inter-microtubule bridge (PubMed:15858577, PubMed:16968737, PubMed:21297582). The TACC3/ch-TOG/clathrin complex is required for the maintenance of kinetochore fiber tension (PubMed:23532825). Plays a role in early autophagosome formation (PubMed:20639872). {ECO:0000269|PubMed:15858577, ECO:0000269|PubMed:16968737, ECO:0000269|PubMed:20639872, ECO:0000269|PubMed:21297582, ECO:0000269|PubMed:23532825}.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
HgeneCLTCchr17:57697534chr17:57775339ENST00000269122-132108_14914.01676.0RegionNote=WD40-like repeat 3
HgeneCLTCchr17:57697534chr17:57775339ENST00000269122-1321213_152214.01676.0RegionInvolved in binding clathrin light chain
HgeneCLTCchr17:57697534chr17:57775339ENST00000269122-132150_19514.01676.0RegionNote=WD40-like repeat 4
HgeneCLTCchr17:57697534chr17:57775339ENST00000269122-1321550_167514.01676.0RegionTrimerization
HgeneCLTCchr17:57697534chr17:57775339ENST00000269122-132196_25714.01676.0RegionNote=WD40-like repeat 5
HgeneCLTCchr17:57697534chr17:57775339ENST00000269122-13224_6714.01676.0RegionNote=WD40-like repeat 1
HgeneCLTCchr17:57697534chr17:57775339ENST00000269122-132258_30114.01676.0RegionNote=WD40-like repeat 6
HgeneCLTCchr17:57697534chr17:57775339ENST00000269122-1322_47914.01676.0RegionNote=Globular terminal domain
HgeneCLTCchr17:57697534chr17:57775339ENST00000269122-132302_33014.01676.0RegionNote=WD40-like repeat 7
HgeneCLTCchr17:57697534chr17:57775339ENST00000269122-132449_46514.01676.0RegionBinding site for the uncoating ATPase%2C involved in lattice disassembly
HgeneCLTCchr17:57697534chr17:57775339ENST00000269122-132480_52314.01676.0RegionNote=Flexible linker
HgeneCLTCchr17:57697534chr17:57775339ENST00000269122-132524_167514.01676.0RegionNote=Heavy chain arm
HgeneCLTCchr17:57697534chr17:57775339ENST00000269122-132524_63414.01676.0RegionNote=Distal segment
HgeneCLTCchr17:57697534chr17:57775339ENST00000269122-132639_167514.01676.0RegionNote=Proximal segment
HgeneCLTCchr17:57697534chr17:57775339ENST00000269122-13268_10714.01676.0RegionNote=WD40-like repeat 2
HgeneCLTCchr17:57697534chr17:57775339ENST00000393043-131108_14914.01640.0RegionNote=WD40-like repeat 3
HgeneCLTCchr17:57697534chr17:57775339ENST00000393043-1311213_152214.01640.0RegionInvolved in binding clathrin light chain
HgeneCLTCchr17:57697534chr17:57775339ENST00000393043-131150_19514.01640.0RegionNote=WD40-like repeat 4
HgeneCLTCchr17:57697534chr17:57775339ENST00000393043-1311550_167514.01640.0RegionTrimerization
HgeneCLTCchr17:57697534chr17:57775339ENST00000393043-131196_25714.01640.0RegionNote=WD40-like repeat 5
HgeneCLTCchr17:57697534chr17:57775339ENST00000393043-13124_6714.01640.0RegionNote=WD40-like repeat 1
HgeneCLTCchr17:57697534chr17:57775339ENST00000393043-131258_30114.01640.0RegionNote=WD40-like repeat 6
HgeneCLTCchr17:57697534chr17:57775339ENST00000393043-1312_47914.01640.0RegionNote=Globular terminal domain
HgeneCLTCchr17:57697534chr17:57775339ENST00000393043-131302_33014.01640.0RegionNote=WD40-like repeat 7
HgeneCLTCchr17:57697534chr17:57775339ENST00000393043-131449_46514.01640.0RegionBinding site for the uncoating ATPase%2C involved in lattice disassembly
HgeneCLTCchr17:57697534chr17:57775339ENST00000393043-131480_52314.01640.0RegionNote=Flexible linker
HgeneCLTCchr17:57697534chr17:57775339ENST00000393043-131524_167514.01640.0RegionNote=Heavy chain arm
HgeneCLTCchr17:57697534chr17:57775339ENST00000393043-131524_63414.01640.0RegionNote=Distal segment
HgeneCLTCchr17:57697534chr17:57775339ENST00000393043-131639_167514.01640.0RegionNote=Proximal segment
HgeneCLTCchr17:57697534chr17:57775339ENST00000393043-13168_10714.01640.0RegionNote=WD40-like repeat 2
HgeneCLTCchr17:57697534chr17:57775339ENST00000269122-1321128_126914.01676.0RepeatCHCR 5
HgeneCLTCchr17:57697534chr17:57775339ENST00000269122-1321274_142014.01676.0RepeatCHCR 6
HgeneCLTCchr17:57697534chr17:57775339ENST00000269122-1321423_156614.01676.0RepeatCHCR 7
HgeneCLTCchr17:57697534chr17:57775339ENST00000269122-132537_68314.01676.0RepeatCHCR 1
HgeneCLTCchr17:57697534chr17:57775339ENST00000269122-132686_82814.01676.0RepeatCHCR 2
HgeneCLTCchr17:57697534chr17:57775339ENST00000269122-132833_97214.01676.0RepeatCHCR 3
HgeneCLTCchr17:57697534chr17:57775339ENST00000269122-132979_112414.01676.0RepeatCHCR 4
HgeneCLTCchr17:57697534chr17:57775339ENST00000393043-1311128_126914.01640.0RepeatCHCR 5
HgeneCLTCchr17:57697534chr17:57775339ENST00000393043-1311274_142014.01640.0RepeatCHCR 6
HgeneCLTCchr17:57697534chr17:57775339ENST00000393043-1311423_156614.01640.0RepeatCHCR 7
HgeneCLTCchr17:57697534chr17:57775339ENST00000393043-131537_68314.01640.0RepeatCHCR 1
HgeneCLTCchr17:57697534chr17:57775339ENST00000393043-131686_82814.01640.0RepeatCHCR 2
HgeneCLTCchr17:57697534chr17:57775339ENST00000393043-131833_97214.01640.0RepeatCHCR 3
HgeneCLTCchr17:57697534chr17:57775339ENST00000393043-131979_112414.01640.0RepeatCHCR 4


Top

Fusion Gene Sequence for CLTC-PTRH2


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.

Top

Fusion Gene PPI Analysis for CLTC-PTRH2


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


Top

Related Drugs for CLTC-PTRH2


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

Top

Related Diseases for CLTC-PTRH2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCLTCC4518356MiT family translocation renal cell carcinoma2ORPHANET
HgeneCLTCC4693389MENTAL RETARDATION, AUTOSOMAL DOMINANT 562GENOMICS_ENGLAND;UNIPROT
HgeneCLTCC0079744Diffuse Large B-Cell Lymphoma1CTD_human
HgeneCLTCC0334121Inflammatory Myofibroblastic Tumor1ORPHANET
TgenePTRH2C4015728NEUROLOGIC, ENDOCRINE, AND PANCREATIC DISEASE, MULTISYSTEM, INFANTILE-ONSET3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgenePTRH2C0033578Prostatic Neoplasms1CTD_human
TgenePTRH2C0376358Malignant neoplasm of prostate1CTD_human