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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:CLN6-ARL6IP5

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: CLN6-ARL6IP5
FusionPDB ID: 17237
FusionGDB2.0 ID: 17237
HgeneTgene
Gene symbol

CLN6

ARL6IP5

Gene ID

54982

10550

Gene nameCLN6 transmembrane ER proteinADP ribosylation factor like GTPase 6 interacting protein 5
SynonymsCLN4A|HsT18960|nclfDERP11|GTRAP3-18|HSPC127|JWA|PRAF3|Yip6b|addicsin|hp22|jmx
Cytomap

15q23

3p14.1

Type of geneprotein-codingprotein-coding
Descriptionceroid-lipofuscinosis neuronal protein 6ceroid-lipofuscinosis neuronal 6 late infantileceroid-lipofuscinosis, neuronal 6, late infantilePRA1 family protein 3ADP-ribosylation factor GTPase 6 interacting protein 5ADP-ribosylation factor-like 6 interacting protein 5ADP-ribosylation factor-like protein 6-interacting protein 5ADP-ribosylation-like factor 6 interacting protein 5ARL-6-inter
Modification date2020032820200313
UniProtAcc

Q9NWW5

O75915

Ensembl transtripts involved in fusion geneENST idsENST00000249806, ENST00000538696, 
ENST00000564752, ENST00000566347, 
ENST00000418702, ENST00000565471, 
ENST00000569336, 
ENST00000273258, 
ENST00000478935, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score12 X 7 X 9=7568 X 7 X 3=168
# samples 128
** MAII scorelog2(12/756*10)=-2.65535182861255
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(8/168*10)=-1.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: CLN6 [Title/Abstract] AND ARL6IP5 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)CLN6(68510874)-ARL6IP5(69150990), # samples:1
Anticipated loss of major functional domain due to fusion event.CLN6-ARL6IP5 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
CLN6-ARL6IP5 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
CLN6-ARL6IP5 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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
TgeneARL6IP5

GO:0008631

intrinsic apoptotic signaling pathway in response to oxidative stress

18387645


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.
all structure

check buttonFusion gene breakpoints across ARL6IP5 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4STADTCGA-BR-8683-01ACLN6chr15

68510874

-ARL6IP5chr3

69150990

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000418702CLN6chr1568510874-ENST00000273258ARL6IP5chr369150990+2105284186674162
ENST00000418702CLN6chr1568510874-ENST00000478935ARL6IP5chr369150990+15302843012100

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
ENST00000418702ENST00000273258CLN6chr1568510874-ARL6IP5chr369150990+0.0095913760.99040866
ENST00000418702ENST00000478935CLN6chr1568510874-ARL6IP5chr369150990+0.60450350.39549646

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>17237_17237_1_CLN6-ARL6IP5_CLN6_chr15_68510874_ENST00000418702_ARL6IP5_chr3_69150990_ENST00000273258_length(amino acids)=162AA_BP=33
MMRLPARLPSTSTSGSTSHCRTGFWTLGVPLPWFLSPFNMILGGIVVVLVFTGFVWAAHNKDVLRRMKKRYPTTFVMVVMLASYFLISMF

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

>17237_17237_2_CLN6-ARL6IP5_CLN6_chr15_68510874_ENST00000418702_ARL6IP5_chr3_69150990_ENST00000478935_length(amino acids)=100AA_BP=
MKGLRNHGNGTPKVQNPVLQCEVEPEVEVEGSRAGSLISAHRAMPGLQEGGAQLRAWAARRSQVLPPPRRLHGCPAGPSALPFRGRDRFS

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

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Fusion Protein Functional Features


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/chr15:68510874/chr3:69150990)
- 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
CLN6

Q9NWW5

ARL6IP5

O75915

FUNCTION: Regulates intracellular concentrations of taurine and glutamate. Negatively modulates SLC1A1/EAAC1 glutamate transport activity by decreasing its affinity for glutamate in a PKC activity-dependent manner. Plays a role in the retention of SLC1A1/EAAC1 in the endoplasmic reticulum. {ECO:0000250|UniProtKB:Q8R5J9, ECO:0000250|UniProtKB:Q9ES40}.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneARL6IP5chr15:68510874chr3:69150990ENST0000027325803103_11758.666666666666664189.0RegionRequired for homodimer formation and heterodimer formation with ARL6IP1
TgeneARL6IP5chr15:68510874chr3:69150990ENST0000027325803136_18858.666666666666664189.0RegionTargeting to endoplasmic reticulum membrane
TgeneARL6IP5chr15:68510874chr3:69150990ENST000002732580378_9358.666666666666664189.0Topological domainCytoplasmic
TgeneARL6IP5chr15:68510874chr3:69150990ENST0000027325803115_13558.666666666666664189.0TransmembraneHelical
TgeneARL6IP5chr15:68510874chr3:69150990ENST000002732580357_7758.666666666666664189.0TransmembraneHelical
TgeneARL6IP5chr15:68510874chr3:69150990ENST000002732580394_11458.666666666666664189.0TransmembraneHelical

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCLN6chr15:68510874chr3:69150990ENST00000249806-27111_13166.0312.0TransmembraneHelical
HgeneCLN6chr15:68510874chr3:69150990ENST00000249806-27179_19966.0312.0TransmembraneHelical
HgeneCLN6chr15:68510874chr3:69150990ENST00000249806-27204_22466.0312.0TransmembraneHelical
HgeneCLN6chr15:68510874chr3:69150990ENST00000249806-27225_24566.0312.0TransmembraneHelical
HgeneCLN6chr15:68510874chr3:69150990ENST00000249806-27260_28066.0312.0TransmembraneHelical
HgeneCLN6chr15:68510874chr3:69150990ENST00000249806-2756_7666.0312.0TransmembraneHelical
HgeneCLN6chr15:68510874chr3:69150990ENST00000249806-2781_10166.0312.0TransmembraneHelical
TgeneARL6IP5chr15:68510874chr3:69150990ENST00000273258031_3558.666666666666664189.0Topological domainCytoplasmic
TgeneARL6IP5chr15:68510874chr3:69150990ENST000002732580336_5658.666666666666664189.0TransmembraneHelical


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
CLN6
ARL6IP5


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to CLN6-ARL6IP5


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to CLN6-ARL6IP5


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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