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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:CLCN3-SMAD1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: CLCN3-SMAD1
FusionPDB ID: 16988
FusionGDB2.0 ID: 16988
HgeneTgene
Gene symbol

CLCN3

SMAD1

Gene ID

1182

4086

Gene namechloride voltage-gated channel 3SMAD family member 1
SynonymsCLC3|ClC-3BSP-1|BSP1|JV4-1|JV41|MADH1|MADR1
Cytomap

4q33

4q31.21

Type of geneprotein-codingprotein-coding
DescriptionH(+)/Cl(-) exchange transporter 3chloride channel 3chloride channel protein 3chloride channel, voltage-sensitive 3chloride transporter ClC-3mothers against decapentaplegic homolog 1MAD, mothers against decapentaplegic homolog 1Mad-related protein 1SMAD, mothers against DPP homolog 1TGF-beta signaling protein 1mothers against DPP homolog 1transforming growth factor-beta signaling protein
Modification date2020031320200322
UniProtAcc

P51790

.
Ensembl transtripts involved in fusion geneENST idsENST00000506924, ENST00000347613, 
ENST00000360642, ENST00000504131, 
ENST00000513761, 		ENST00000302085, 
ENST00000394092, ENST00000515385, 
ENST00000515527, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score13 X 9 X 6=7026 X 6 X 6=216
# samples 167
** MAII scorelog2(16/702*10)=-2.1333991254172
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/216*10)=-1.6256044852185
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: CLCN3 [Title/Abstract] AND SMAD1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)CLCN3(170557239)-SMAD1(146474936), # samples:3
Anticipated loss of major functional domain due to fusion event.CLCN3-SMAD1 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.
CLCN3-SMAD1 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.
CLCN3-SMAD1 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.
CLCN3-SMAD1 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.
CLCN3-SMAD1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
CLCN3-SMAD1 seems lost the major protein functional domain in Tgene partner, which is a transcription factor 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
HgeneCLCN3

GO:1902476

chloride transmembrane transport

11274166

TgeneSMAD1

GO:0007183

SMAD protein complex assembly

9111321

TgeneSMAD1

GO:0010628

positive regulation of gene expression

19664780

TgeneSMAD1

GO:0030509

BMP signaling pathway

8653785|9389648|18548003

TgeneSMAD1

GO:0045944

positive regulation of transcription by RNA polymerase II

12270938


check buttonFusion gene breakpoints across CLCN3 (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 SMAD1 (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
ChimerDB4BRCATCGA-AN-A04C-01ACLCN3chr4

170557239

-SMAD1chr4

146474936

+
ChimerDB4BRCATCGA-AN-A04C-01ACLCN3chr4

170557239

+SMAD1chr4

146474936

+
ChimerDB4BRCATCGA-AN-A04CCLCN3chr4

170557239

+SMAD1chr4

146474935

+


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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)
ENST00000513761CLCN3chr4170557239+ENST00000302085SMAD1chr4146474936+12657195591119186
ENST00000347613CLCN3chr4170557239+ENST00000302085SMAD1chr4146474936+12607145541114186
ENST00000360642CLCN3chr4170557239+ENST00000302085SMAD1chr4146474936+12577115511111186
ENST00000513761CLCN3chr4170557239+ENST00000302085SMAD1chr4146474935+12657195591119186
ENST00000347613CLCN3chr4170557239+ENST00000302085SMAD1chr4146474935+12607145541114186
ENST00000360642CLCN3chr4170557239+ENST00000302085SMAD1chr4146474935+12577115511111186

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
ENST00000513761ENST00000302085CLCN3chr4170557239+SMAD1chr4146474936+0.0027724640.9972275
ENST00000347613ENST00000302085CLCN3chr4170557239+SMAD1chr4146474936+0.002845710.99715424
ENST00000360642ENST00000302085CLCN3chr4170557239+SMAD1chr4146474936+0.0034877220.99651223
ENST00000513761ENST00000302085CLCN3chr4170557239+SMAD1chr4146474935+0.0027724640.9972275
ENST00000347613ENST00000302085CLCN3chr4170557239+SMAD1chr4146474935+0.002845710.99715424
ENST00000360642ENST00000302085CLCN3chr4170557239+SMAD1chr4146474935+0.0034877220.99651223

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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

>16988_16988_1_CLCN3-SMAD1_CLCN3_chr4_170557239_ENST00000347613_SMAD1_chr4_146474935_ENST00000302085_length(amino acids)=186AA_BP=53
MESEQLFHRGYYRNSYNSITSASSDEELLDGAGVIMDFQTSEDDNLLDGDTAVGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPT
TVCKIPSGCSLKIFNNQEFAQLLAQSVNHGFETVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHN

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

>16988_16988_2_CLCN3-SMAD1_CLCN3_chr4_170557239_ENST00000347613_SMAD1_chr4_146474936_ENST00000302085_length(amino acids)=186AA_BP=53
MESEQLFHRGYYRNSYNSITSASSDEELLDGAGVIMDFQTSEDDNLLDGDTAVGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPT
TVCKIPSGCSLKIFNNQEFAQLLAQSVNHGFETVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHN

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

>16988_16988_3_CLCN3-SMAD1_CLCN3_chr4_170557239_ENST00000360642_SMAD1_chr4_146474935_ENST00000302085_length(amino acids)=186AA_BP=53
MESEQLFHRGYYRNSYNSITSASSDEELLDGAGVIMDFQTSEDDNLLDGDTAVGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPT
TVCKIPSGCSLKIFNNQEFAQLLAQSVNHGFETVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHN

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

>16988_16988_4_CLCN3-SMAD1_CLCN3_chr4_170557239_ENST00000360642_SMAD1_chr4_146474936_ENST00000302085_length(amino acids)=186AA_BP=53
MESEQLFHRGYYRNSYNSITSASSDEELLDGAGVIMDFQTSEDDNLLDGDTAVGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPT
TVCKIPSGCSLKIFNNQEFAQLLAQSVNHGFETVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHN

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

>16988_16988_5_CLCN3-SMAD1_CLCN3_chr4_170557239_ENST00000513761_SMAD1_chr4_146474935_ENST00000302085_length(amino acids)=186AA_BP=53
MESEQLFHRGYYRNSYNSITSASSDEELLDGAGVIMDFQTSEDDNLLDGDTAVGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPT
TVCKIPSGCSLKIFNNQEFAQLLAQSVNHGFETVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHN

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

>16988_16988_6_CLCN3-SMAD1_CLCN3_chr4_170557239_ENST00000513761_SMAD1_chr4_146474936_ENST00000302085_length(amino acids)=186AA_BP=53
MESEQLFHRGYYRNSYNSITSASSDEELLDGAGVIMDFQTSEDDNLLDGDTAVGVHLYYVGGEVYAECLSDSSIFVQSRNCNYHHGFHPT
TVCKIPSGCSLKIFNNQEFAQLLAQSVNHGFETVYELTKMCTIRMSFVKGWGAEYHRQDVTSTPCWIEIHLHGPLQWLDKVLTQMGSPHN

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

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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/chr4:170557239/chr4:146474936)
- 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
CLCN3

P51790

.
FUNCTION: [Isoform 1]: Strongly outwardly rectifying, electrogenic H(+)/Cl(-)exchanger which mediates the exchange of chloride ions against protons (By similarity). The CLC channel family contains both chloride channels and proton-coupled anion transporters that exchange chloride or another anion for protons (PubMed:29845874). The presence of conserved gating glutamate residues is typical for family members that function as antiporters (PubMed:29845874). {ECO:0000250|UniProtKB:P51791, ECO:0000303|PubMed:29845874}.; FUNCTION: [Isoform 2]: Strongly outwardly rectifying, electrogenic H(+)/Cl(-)exchanger which mediates the exchange of chloride ions against protons. {ECO:0000269|PubMed:11967229}.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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+21428_2953.333333333333336867.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+21446_4753.333333333333336867.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+21228_2953.333333333333336792.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+21246_4753.333333333333336792.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+21328_2953.333333333333336819.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+21346_4753.333333333333336819.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+21428_2953.333333333333336867.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+21446_4753.333333333333336867.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+21228_2953.333333333333336792.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+21246_4753.333333333333336792.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+21328_2953.333333333333336819.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+21346_4753.333333333333336819.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
TgeneSMAD1chr4:170557239chr4:146474935ENST0000030208547418_428332.3333333333333466.0RegionL3 loop
TgeneSMAD1chr4:170557239chr4:146474935ENST0000039409247418_428332.3333333333333466.0RegionL3 loop
TgeneSMAD1chr4:170557239chr4:146474935ENST0000051538547418_428332.3333333333333466.0RegionL3 loop
TgeneSMAD1chr4:170557239chr4:146474936ENST0000030208547418_428332.3333333333333466.0RegionL3 loop
TgeneSMAD1chr4:170557239chr4:146474936ENST0000039409247418_428332.3333333333333466.0RegionL3 loop
TgeneSMAD1chr4:170557239chr4:146474936ENST0000051538547418_428332.3333333333333466.0RegionL3 loop

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214658_72253.333333333333336867.0DomainCBS 1
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214755_81253.333333333333336867.0DomainCBS 2
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212658_72253.333333333333336792.0DomainCBS 1
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212755_81253.333333333333336792.0DomainCBS 2
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213658_72253.333333333333336819.0DomainCBS 1
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213755_81253.333333333333336819.0DomainCBS 2
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214658_72253.333333333333336867.0DomainCBS 1
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214755_81253.333333333333336867.0DomainCBS 2
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212658_72253.333333333333336792.0DomainCBS 1
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212755_81253.333333333333336792.0DomainCBS 2
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213658_72253.333333333333336819.0DomainCBS 1
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213755_81253.333333333333336819.0DomainCBS 2
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214241_24853.333333333333336867.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214313_32553.333333333333336867.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214329_33753.333333333333336867.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214572_58653.333333333333336867.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214590_60153.333333333333336867.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214602_60553.333333333333336867.0IntramembraneNote%3DLoop between two helices
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212241_24853.333333333333336792.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212313_32553.333333333333336792.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212329_33753.333333333333336792.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212572_58653.333333333333336792.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212590_60153.333333333333336792.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212602_60553.333333333333336792.0IntramembraneNote%3DLoop between two helices
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213241_24853.333333333333336819.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213313_32553.333333333333336819.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213329_33753.333333333333336819.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213572_58653.333333333333336819.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213590_60153.333333333333336819.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213602_60553.333333333333336819.0IntramembraneNote%3DLoop between two helices
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214241_24853.333333333333336867.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214313_32553.333333333333336867.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214329_33753.333333333333336867.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214572_58653.333333333333336867.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214590_60153.333333333333336867.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214602_60553.333333333333336867.0IntramembraneNote%3DLoop between two helices
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212241_24853.333333333333336792.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212313_32553.333333333333336792.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212329_33753.333333333333336792.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212572_58653.333333333333336792.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212590_60153.333333333333336792.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212602_60553.333333333333336792.0IntramembraneNote%3DLoop between two helices
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213241_24853.333333333333336819.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213313_32553.333333333333336819.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213329_33753.333333333333336819.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213572_58653.333333333333336819.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213590_60153.333333333333336819.0IntramembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213602_60553.333333333333336819.0IntramembraneNote%3DLoop between two helices
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214238_24253.333333333333336867.0MotifSelectivity filter part_1
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214280_28453.333333333333336867.0MotifSelectivity filter part_2
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214525_52953.333333333333336867.0MotifSelectivity filter part_3
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+21471_7553.333333333333336867.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212238_24253.333333333333336792.0MotifSelectivity filter part_1
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212280_28453.333333333333336792.0MotifSelectivity filter part_2
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212525_52953.333333333333336792.0MotifSelectivity filter part_3
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+21271_7553.333333333333336792.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213238_24253.333333333333336819.0MotifSelectivity filter part_1
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213280_28453.333333333333336819.0MotifSelectivity filter part_2
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213525_52953.333333333333336819.0MotifSelectivity filter part_3
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+21371_7553.333333333333336819.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214238_24253.333333333333336867.0MotifSelectivity filter part_1
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214280_28453.333333333333336867.0MotifSelectivity filter part_2
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214525_52953.333333333333336867.0MotifSelectivity filter part_3
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+21471_7553.333333333333336867.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212238_24253.333333333333336792.0MotifSelectivity filter part_1
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212280_28453.333333333333336792.0MotifSelectivity filter part_2
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212525_52953.333333333333336792.0MotifSelectivity filter part_3
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+21271_7553.333333333333336792.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213238_24253.333333333333336819.0MotifSelectivity filter part_1
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213280_28453.333333333333336819.0MotifSelectivity filter part_2
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213525_52953.333333333333336819.0MotifSelectivity filter part_3
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+21371_7553.333333333333336819.0MotifDi-leucine internalization motif%3B mediates targeting to late endosome and lysosome membranes
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214689_69153.333333333333336867.0Nucleotide bindingATP
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214796_79953.333333333333336867.0Nucleotide bindingATP
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212689_69153.333333333333336792.0Nucleotide bindingATP
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212796_79953.333333333333336792.0Nucleotide bindingATP
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213689_69153.333333333333336819.0Nucleotide bindingATP
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213796_79953.333333333333336819.0Nucleotide bindingATP
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214689_69153.333333333333336867.0Nucleotide bindingATP
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214796_79953.333333333333336867.0Nucleotide bindingATP
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212689_69153.333333333333336792.0Nucleotide bindingATP
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212796_79953.333333333333336792.0Nucleotide bindingATP
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213689_69153.333333333333336819.0Nucleotide bindingATP
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213796_79953.333333333333336819.0Nucleotide bindingATP
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+2141_12553.333333333333336867.0Topological domainCytoplasmic
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214625_81853.333333333333336867.0Topological domainCytoplasmic
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+2121_12553.333333333333336792.0Topological domainCytoplasmic
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212625_81853.333333333333336792.0Topological domainCytoplasmic
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+2131_12553.333333333333336819.0Topological domainCytoplasmic
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213625_81853.333333333333336819.0Topological domainCytoplasmic
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+2141_12553.333333333333336867.0Topological domainCytoplasmic
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214625_81853.333333333333336867.0Topological domainCytoplasmic
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+2121_12553.333333333333336792.0Topological domainCytoplasmic
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212625_81853.333333333333336792.0Topological domainCytoplasmic
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+2131_12553.333333333333336819.0Topological domainCytoplasmic
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213625_81853.333333333333336819.0Topological domainCytoplasmic
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214126_16353.333333333333336867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214209_23253.333333333333336867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214258_27653.333333333333336867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214282_30153.333333333333336867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214349_36753.333333333333336867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214391_41653.333333333333336867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214423_44353.333333333333336867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214500_52053.333333333333336867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214525_54453.333333333333336867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000347613+214606_62453.333333333333336867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212126_16353.333333333333336792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212209_23253.333333333333336792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212258_27653.333333333333336792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212282_30153.333333333333336792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212349_36753.333333333333336792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212391_41653.333333333333336792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212423_44353.333333333333336792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212500_52053.333333333333336792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212525_54453.333333333333336792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000360642+212606_62453.333333333333336792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213126_16353.333333333333336819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213209_23253.333333333333336819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213258_27653.333333333333336819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213282_30153.333333333333336819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213349_36753.333333333333336819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213391_41653.333333333333336819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213423_44353.333333333333336819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213500_52053.333333333333336819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213525_54453.333333333333336819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474935ENST00000513761+213606_62453.333333333333336819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214126_16353.333333333333336867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214209_23253.333333333333336867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214258_27653.333333333333336867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214282_30153.333333333333336867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214349_36753.333333333333336867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214391_41653.333333333333336867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214423_44353.333333333333336867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214500_52053.333333333333336867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214525_54453.333333333333336867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000347613+214606_62453.333333333333336867.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212126_16353.333333333333336792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212209_23253.333333333333336792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212258_27653.333333333333336792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212282_30153.333333333333336792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212349_36753.333333333333336792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212391_41653.333333333333336792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212423_44353.333333333333336792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212500_52053.333333333333336792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212525_54453.333333333333336792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000360642+212606_62453.333333333333336792.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213126_16353.333333333333336819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213209_23253.333333333333336819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213258_27653.333333333333336819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213282_30153.333333333333336819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213349_36753.333333333333336819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213391_41653.333333333333336819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213423_44353.333333333333336819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213500_52053.333333333333336819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213525_54453.333333333333336819.0TransmembraneHelical
HgeneCLCN3chr4:170557239chr4:146474936ENST00000513761+213606_62453.333333333333336819.0TransmembraneHelical
TgeneSMAD1chr4:170557239chr4:146474935ENST0000030208547198_201332.3333333333333466.0Compositional biasNote=Poly-Ser
TgeneSMAD1chr4:170557239chr4:146474935ENST000003020854739_45332.3333333333333466.0Compositional biasNote=Poly-Lys
TgeneSMAD1chr4:170557239chr4:146474935ENST0000039409247198_201332.3333333333333466.0Compositional biasNote=Poly-Ser
TgeneSMAD1chr4:170557239chr4:146474935ENST000003940924739_45332.3333333333333466.0Compositional biasNote=Poly-Lys
TgeneSMAD1chr4:170557239chr4:146474935ENST0000051538547198_201332.3333333333333466.0Compositional biasNote=Poly-Ser
TgeneSMAD1chr4:170557239chr4:146474935ENST000005153854739_45332.3333333333333466.0Compositional biasNote=Poly-Lys
TgeneSMAD1chr4:170557239chr4:146474936ENST0000030208547198_201332.3333333333333466.0Compositional biasNote=Poly-Ser
TgeneSMAD1chr4:170557239chr4:146474936ENST000003020854739_45332.3333333333333466.0Compositional biasNote=Poly-Lys
TgeneSMAD1chr4:170557239chr4:146474936ENST0000039409247198_201332.3333333333333466.0Compositional biasNote=Poly-Ser
TgeneSMAD1chr4:170557239chr4:146474936ENST000003940924739_45332.3333333333333466.0Compositional biasNote=Poly-Lys
TgeneSMAD1chr4:170557239chr4:146474936ENST0000051538547198_201332.3333333333333466.0Compositional biasNote=Poly-Ser
TgeneSMAD1chr4:170557239chr4:146474936ENST000005153854739_45332.3333333333333466.0Compositional biasNote=Poly-Lys
TgeneSMAD1chr4:170557239chr4:146474935ENST000003020854712_136332.3333333333333466.0DomainMH1
TgeneSMAD1chr4:170557239chr4:146474935ENST0000030208547271_465332.3333333333333466.0DomainMH2
TgeneSMAD1chr4:170557239chr4:146474935ENST000003940924712_136332.3333333333333466.0DomainMH1
TgeneSMAD1chr4:170557239chr4:146474935ENST0000039409247271_465332.3333333333333466.0DomainMH2
TgeneSMAD1chr4:170557239chr4:146474935ENST000005153854712_136332.3333333333333466.0DomainMH1
TgeneSMAD1chr4:170557239chr4:146474935ENST0000051538547271_465332.3333333333333466.0DomainMH2
TgeneSMAD1chr4:170557239chr4:146474936ENST000003020854712_136332.3333333333333466.0DomainMH1
TgeneSMAD1chr4:170557239chr4:146474936ENST0000030208547271_465332.3333333333333466.0DomainMH2
TgeneSMAD1chr4:170557239chr4:146474936ENST000003940924712_136332.3333333333333466.0DomainMH1
TgeneSMAD1chr4:170557239chr4:146474936ENST0000039409247271_465332.3333333333333466.0DomainMH2
TgeneSMAD1chr4:170557239chr4:146474936ENST000005153854712_136332.3333333333333466.0DomainMH1
TgeneSMAD1chr4:170557239chr4:146474936ENST0000051538547271_465332.3333333333333466.0DomainMH2


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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
CLCN3
SMAD1


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 CLCN3-SMAD1


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 CLCN3-SMAD1


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