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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:CLTC-FAM129C (FusionGDB2 ID:HG1213TG199786)

Fusion Gene Summary for CLTC-FAM129C

check button Fusion gene summary
Fusion gene informationFusion gene name: CLTC-FAM129C
Fusion gene ID: hg1213tg199786
HgeneTgene
Gene symbol

CLTC

FAM129C

Gene ID

1213

199786

Gene nameclathrin heavy chainniban apoptosis regulator 3
SynonymsCHC|CHC17|CLH-17|CLTCL2|Hc|MRD56BCNP1|FAM129C
Cytomap('CLTC')('FAM129C')

17q23.1

19p13.11

Type of geneprotein-codingprotein-coding
Descriptionclathrin heavy chain 1clathrin heavy chain on chromosome 17clathrin, heavy polypeptide (Hc)clathrin, heavy polypeptide-like 2protein Niban 3B-cell novel protein 1family with sequence similarity 129 member Cniban-like protein 2
Modification date2020031320200313
UniProtAcc

Q00610

.
Ensembl transtripts involved in fusion geneENST00000269122, ENST00000393043, 
ENST00000579456, ENST00000579815, 
Fusion gene scores* DoF score27 X 40 X 17=183605 X 4 X 4=80
# samples 844
** MAII scorelog2(84/18360*10)=-4.45003292063505
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/80*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CLTC [Title/Abstract] AND FAM129C [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCLTC(57697534)-FAM129C(17648185), # samples:3
Anticipated loss of major functional domain due to fusion event.CLTC-FAM129C seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
CLTC-FAM129C seems lost the major protein functional domain in Hgene 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 button Fusion gene information
* 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-AN-A0FD-01ACLTCchr17

57697534

-FAM129Cchr19

17648185

+
ChimerDB4BRCATCGA-AN-A0FD-01ACLTCchr17

57697534

+FAM129Cchr19

17648185

+


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Fusion Gene ORF analysis for CLTC-FAM129C

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
5CDS-3UTRENST00000269122ENST00000597887CLTCchr17

57697534

+FAM129Cchr19

17648185

+
5CDS-3UTRENST00000393043ENST00000597887CLTCchr17

57697534

+FAM129Cchr19

17648185

+
5CDS-3UTRENST00000579456ENST00000597887CLTCchr17

57697534

+FAM129Cchr19

17648185

+
5CDS-5UTRENST00000269122ENST00000449408CLTCchr17

57697534

+FAM129Cchr19

17648185

+
5CDS-5UTRENST00000269122ENST00000599124CLTCchr17

57697534

+FAM129Cchr19

17648185

+
5CDS-5UTRENST00000269122ENST00000600871CLTCchr17

57697534

+FAM129Cchr19

17648185

+
5CDS-5UTRENST00000393043ENST00000449408CLTCchr17

57697534

+FAM129Cchr19

17648185

+
5CDS-5UTRENST00000393043ENST00000599124CLTCchr17

57697534

+FAM129Cchr19

17648185

+
5CDS-5UTRENST00000393043ENST00000600871CLTCchr17

57697534

+FAM129Cchr19

17648185

+
5CDS-5UTRENST00000579456ENST00000449408CLTCchr17

57697534

+FAM129Cchr19

17648185

+
5CDS-5UTRENST00000579456ENST00000599124CLTCchr17

57697534

+FAM129Cchr19

17648185

+
5CDS-5UTRENST00000579456ENST00000600871CLTCchr17

57697534

+FAM129Cchr19

17648185

+
Frame-shiftENST00000269122ENST00000300971CLTCchr17

57697534

+FAM129Cchr19

17648185

+
Frame-shiftENST00000269122ENST00000332386CLTCchr17

57697534

+FAM129Cchr19

17648185

+
Frame-shiftENST00000269122ENST00000335393CLTCchr17

57697534

+FAM129Cchr19

17648185

+
Frame-shiftENST00000269122ENST00000352727CLTCchr17

57697534

+FAM129Cchr19

17648185

+
Frame-shiftENST00000269122ENST00000595684CLTCchr17

57697534

+FAM129Cchr19

17648185

+
Frame-shiftENST00000269122ENST00000599164CLTCchr17

57697534

+FAM129Cchr19

17648185

+
Frame-shiftENST00000269122ENST00000601861CLTCchr17

57697534

+FAM129Cchr19

17648185

+
Frame-shiftENST00000393043ENST00000300971CLTCchr17

57697534

+FAM129Cchr19

17648185

+
Frame-shiftENST00000393043ENST00000332386CLTCchr17

57697534

+FAM129Cchr19

17648185

+
Frame-shiftENST00000393043ENST00000335393CLTCchr17

57697534

+FAM129Cchr19

17648185

+
Frame-shiftENST00000393043ENST00000352727CLTCchr17

57697534

+FAM129Cchr19

17648185

+
Frame-shiftENST00000393043ENST00000595684CLTCchr17

57697534

+FAM129Cchr19

17648185

+
Frame-shiftENST00000393043ENST00000599164CLTCchr17

57697534

+FAM129Cchr19

17648185

+
Frame-shiftENST00000393043ENST00000601861CLTCchr17

57697534

+FAM129Cchr19

17648185

+
Frame-shiftENST00000579456ENST00000300971CLTCchr17

57697534

+FAM129Cchr19

17648185

+
Frame-shiftENST00000579456ENST00000332386CLTCchr17

57697534

+FAM129Cchr19

17648185

+
Frame-shiftENST00000579456ENST00000335393CLTCchr17

57697534

+FAM129Cchr19

17648185

+
Frame-shiftENST00000579456ENST00000352727CLTCchr17

57697534

+FAM129Cchr19

17648185

+
Frame-shiftENST00000579456ENST00000595684CLTCchr17

57697534

+FAM129Cchr19

17648185

+
Frame-shiftENST00000579456ENST00000599164CLTCchr17

57697534

+FAM129Cchr19

17648185

+
Frame-shiftENST00000579456ENST00000601861CLTCchr17

57697534

+FAM129Cchr19

17648185

+
intron-3CDSENST00000579815ENST00000300971CLTCchr17

57697534

+FAM129Cchr19

17648185

+
intron-3CDSENST00000579815ENST00000332386CLTCchr17

57697534

+FAM129Cchr19

17648185

+
intron-3CDSENST00000579815ENST00000335393CLTCchr17

57697534

+FAM129Cchr19

17648185

+
intron-3CDSENST00000579815ENST00000352727CLTCchr17

57697534

+FAM129Cchr19

17648185

+
intron-3CDSENST00000579815ENST00000595684CLTCchr17

57697534

+FAM129Cchr19

17648185

+
intron-3CDSENST00000579815ENST00000599164CLTCchr17

57697534

+FAM129Cchr19

17648185

+
intron-3CDSENST00000579815ENST00000601861CLTCchr17

57697534

+FAM129Cchr19

17648185

+
intron-3UTRENST00000579815ENST00000597887CLTCchr17

57697534

+FAM129Cchr19

17648185

+
intron-5UTRENST00000579815ENST00000449408CLTCchr17

57697534

+FAM129Cchr19

17648185

+
intron-5UTRENST00000579815ENST00000599124CLTCchr17

57697534

+FAM129Cchr19

17648185

+
intron-5UTRENST00000579815ENST00000600871CLTCchr17

57697534

+FAM129Cchr19

17648185

+

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 CLTC-FAM129C


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)
CLTCchr1757697534+FAM129Cchr1917648184+2.16E-091
CLTCchr1757697534+FAM129Cchr1917648184+2.16E-091


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.
genomic feature of top 1%

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Fusion Protein Features for CLTC-FAM129C


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/:57697534/:17648185)
- 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
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: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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 CLTC-FAM129C


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 CLTC-FAM129C


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 CLTC-FAM129C


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 CLTC-FAM129C


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