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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:CLN6-RPL4 (FusionGDB2 ID:17268)

Fusion Gene Summary for CLN6-RPL4

check button Fusion gene summary
Fusion gene informationFusion gene name: CLN6-RPL4
Fusion gene ID: 17268
HgeneTgene
Gene symbol

CLN6

RPL4

Gene ID

54982

6124

Gene nameCLN6 transmembrane ER proteinribosomal protein L4
SynonymsCLN4A|HsT18960|nclfL4
Cytomap

15q23

15q22.31

Type of geneprotein-codingprotein-coding
Descriptionceroid-lipofuscinosis neuronal protein 6ceroid-lipofuscinosis neuronal 6 late infantileceroid-lipofuscinosis, neuronal 6, late infantile60S ribosomal protein L460S ribosomal protein L1large ribosomal subunit protein uL4
Modification date2020032820200327
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000249806, ENST00000565471, 
ENST00000418702, ENST00000566347, 
ENST00000538696, ENST00000564752, 
ENST00000569336, 		ENST00000307961, 
ENST00000568588, ENST00000564517, 
Fusion gene scores* DoF score12 X 7 X 9=75616 X 14 X 5=1120
# samples 1217
** MAII scorelog2(12/756*10)=-2.65535182861255
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(17/1120*10)=-2.71989208080726
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CLN6 [Title/Abstract] AND RPL4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCLN6(68510873)-RPL4(66791990), # samples:1
Anticipated loss of major functional domain due to fusion event.CLN6-RPL4 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
CLN6-RPL4 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

check buttonFusion gene breakpoints across CLN6 (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 RPL4 (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
ChimerDB4LUSCTCGA-21-1070CLN6chr15

68510873

-RPL4chr15

66791990

-


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Fusion Gene ORF analysis for CLN6-RPL4

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-shiftENST00000249806ENST00000307961CLN6chr15

68510873

-RPL4chr15

66791990

-
Frame-shiftENST00000249806ENST00000568588CLN6chr15

68510873

-RPL4chr15

66791990

-
5CDS-intronENST00000249806ENST00000564517CLN6chr15

68510873

-RPL4chr15

66791990

-
intron-3CDSENST00000565471ENST00000307961CLN6chr15

68510873

-RPL4chr15

66791990

-
intron-3CDSENST00000565471ENST00000568588CLN6chr15

68510873

-RPL4chr15

66791990

-
intron-intronENST00000565471ENST00000564517CLN6chr15

68510873

-RPL4chr15

66791990

-
Frame-shiftENST00000418702ENST00000307961CLN6chr15

68510873

-RPL4chr15

66791990

-
In-frameENST00000418702ENST00000568588CLN6chr15

68510873

-RPL4chr15

66791990

-
5CDS-intronENST00000418702ENST00000564517CLN6chr15

68510873

-RPL4chr15

66791990

-
Frame-shiftENST00000566347ENST00000307961CLN6chr15

68510873

-RPL4chr15

66791990

-
Frame-shiftENST00000566347ENST00000568588CLN6chr15

68510873

-RPL4chr15

66791990

-
5CDS-intronENST00000566347ENST00000564517CLN6chr15

68510873

-RPL4chr15

66791990

-
Frame-shiftENST00000538696ENST00000307961CLN6chr15

68510873

-RPL4chr15

66791990

-
Frame-shiftENST00000538696ENST00000568588CLN6chr15

68510873

-RPL4chr15

66791990

-
5CDS-intronENST00000538696ENST00000564517CLN6chr15

68510873

-RPL4chr15

66791990

-
Frame-shiftENST00000564752ENST00000307961CLN6chr15

68510873

-RPL4chr15

66791990

-
Frame-shiftENST00000564752ENST00000568588CLN6chr15

68510873

-RPL4chr15

66791990

-
5CDS-intronENST00000564752ENST00000564517CLN6chr15

68510873

-RPL4chr15

66791990

-
intron-3CDSENST00000569336ENST00000307961CLN6chr15

68510873

-RPL4chr15

66791990

-
intron-3CDSENST00000569336ENST00000568588CLN6chr15

68510873

-RPL4chr15

66791990

-
intron-intronENST00000569336ENST00000564517CLN6chr15

68510873

-RPL4chr15

66791990

-

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)
ENST00000418702CLN6chr1568510873-ENST00000568588RPL4chr1566791990-61428486529147

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
ENST00000418702ENST00000568588CLN6chr1568510873-RPL4chr1566791990-0.0047286640.9952714

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Fusion Genomic Features for CLN6-RPL4


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.

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Fusion Protein Features for CLN6-RPL4


check button Go to

FGviewer for the breakpoints of chr15:68510873-chr15:66791990

.
- 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
TgeneRPL4chr15:68510873chr15:66791990ENST00000307961810364_427346.0428.0Compositional biasNote=Lys-rich

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCLN6chr15:68510873chr15:66791990ENST00000249806-27111_13166.0312.0TransmembraneHelical
HgeneCLN6chr15:68510873chr15:66791990ENST00000249806-27179_19966.0312.0TransmembraneHelical
HgeneCLN6chr15:68510873chr15:66791990ENST00000249806-27204_22466.0312.0TransmembraneHelical
HgeneCLN6chr15:68510873chr15:66791990ENST00000249806-27225_24566.0312.0TransmembraneHelical
HgeneCLN6chr15:68510873chr15:66791990ENST00000249806-27260_28066.0312.0TransmembraneHelical
HgeneCLN6chr15:68510873chr15:66791990ENST00000249806-2756_7666.0312.0TransmembraneHelical
HgeneCLN6chr15:68510873chr15:66791990ENST00000249806-2781_10166.0312.0TransmembraneHelical


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Fusion Gene Sequence for CLN6-RPL4


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_ENST00000418702_ENST00000568588_TCGA-21-1070_CLN6_chr15_68510873_-_RPL4_chr15_66791990_length(transcript)=614nt_BP=284nt
GAATTTGCGGCGGCCTCCGCCGGGGCAGCCGAGCTGAACCGGTCTCTTCCTCGGAAAGGCAGGGCCGAGGGGCCTGCGGGGCAGCCATGG
AGGCGACGCGGAGGCGGCAGCACCTGGGAGCGACGGGCGGCCCAGGCGCGCAGCTGGGCGCCTCCTTCCTGCAGGCCAGGCATGGCTCTG
TGAGCGCTGATGAGGCTGCCCGCACGGCTCCCTTCCACCTCGACCTCTGGTTCTACTTCACACTGCAGAACTGGGTTCTGGACTTTGGGC
GTCCCATTGCCATGCACAAGCTCCGGGTGGATAAGGCAGCTGCTGCAGCAGCGGCACTACAAGCCAAATCAGATGAGAAGGCGGCGGTTG
CAGGCAAGAAGCCTGTGGTAGGTAAGAAAGGAAAGAAGGCTGCTGTTGGTGTTAAGAAGCAGAAGAAGCCTCTGGTGGGAAAAAAGGCAG
CAGCTACCAAGAAACCAGCCCCTGAAAAGAAGCCTGCAGAGAAGAAACCTACTACAGAGGAGAAGAAGCCTGCTGCATAAACTCTTAAAT

>In-frame_ENST00000418702_ENST00000568588_TCGA-21-1070_CLN6_chr15_68510873_-_RPL4_chr15_66791990_length(amino acids)=147AA_start in transcript=86_stop in transcript=529
MEATRRRQHLGATGGPGAQLGASFLQARHGSVSADEAARTAPFHLDLWFYFTLQNWVLDFGRPIAMHKLRVDKAAAAAAALQAKSDEKAA

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

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Fusion Gene PPI Analysis for CLN6-RPL4


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 CLN6-RPL4


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 CLN6-RPL4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCLN6C1866282CEROID LIPOFUSCINOSIS, NEURONAL, 69CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCLN6C0022797Adult Neuronal Ceroid Lipofuscinosis5CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCLN6C0011757Developmental Coordination Disorder1CTD_human
HgeneCLN6C0018975Hemeralopia1CTD_human
HgeneCLN6C0021368Inflammation1CTD_human
HgeneCLN6C0022340Late-Infantile Neuronal Ceroid Lipfuscinosis1CTD_human
HgeneCLN6C0026613Motor Skills Disorders1CTD_human
HgeneCLN6C0027877Neuronal Ceroid-Lipofuscinoses1CTD_human
HgeneCLN6C0042790Vision Disorders1CTD_human
HgeneCLN6C0233769Micropsia1CTD_human
HgeneCLN6C0233771Macropsia1CTD_human
HgeneCLN6C0268281Infantile neuronal ceroid lipofuscinosis1CTD_human
HgeneCLN6C0271185Metamorphopsia1CTD_human
HgeneCLN6C0333641Atrophic1CTD_human
HgeneCLN6C0751383Juvenile Neuronal Ceroid Lipofuscinosis1CTD_human
HgeneCLN6C0751776Atypical Inclusion-Body Disease1CTD_human
HgeneCLN6C0751777Familial Progressive Myoclonic Epilepsy1CTD_human
HgeneCLN6C0751778Myoclonic Epilepsies, Progressive1CTD_human
HgeneCLN6C0751779Action Myoclonus-Renal Failure Syndrome1CTD_human
HgeneCLN6C0751780Biotin-Responsive Encephalopathy1CTD_human
HgeneCLN6C0751781Dentatorubral-Pallidoluysian Atrophy1CTD_human
HgeneCLN6C0751782May-White Syndrome1CTD_human
HgeneCLN6C1262477Weight decreased1CTD_human
HgeneCLN6C1834207Ceroid Lipofuscinosis, Neuronal, Parry Type1CTD_human
HgeneCLN6C3489704Vision Disability1CTD_human
HgeneCLN6C3665347Visual Impairment1CTD_human