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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:ADAMTS9-CHL1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ADAMTS9-CHL1
FusionPDB ID: 2112
FusionGDB2.0 ID: 2112
HgeneTgene
Gene symbol

ADAMTS9

CHL1

Gene ID

56999

10752

Gene nameADAM metallopeptidase with thrombospondin type 1 motif 9cell adhesion molecule L1 like
Synonyms-CALL|L1CAM2
Cytomap

3p14.1

3p26.3

Type of geneprotein-codingprotein-coding
DescriptionA disintegrin and metalloproteinase with thrombospondin motifs 9a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9neural cell adhesion molecule L1-like proteinL1 cell adhesion molecule 2cell adhesion molecule with homology to L1CAM (close homolog of L1)cell adhesion molecule with homology to L1CAM (close homologue of L1)close homolog of L1
Modification date2020031320200313
UniProtAcc

Q9P2N4

O00533

Ensembl transtripts involved in fusion geneENST idsENST00000295903, ENST00000498707, 
ENST00000459780, ENST00000467257, 
ENST00000489224, ENST00000256509, 
ENST00000397491, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score7 X 7 X 5=2455 X 7 X 4=140
# samples 76
** MAII scorelog2(7/245*10)=-1.8073549220576
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/140*10)=-1.22239242133645
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: ADAMTS9 [Title/Abstract] AND CHL1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ADAMTS9(64619374)-CHL1(447178), # samples:1
Anticipated loss of major functional domain due to fusion event.ADAMTS9-CHL1 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.
ADAMTS9-CHL1 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.
ADAMTS9-CHL1 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.
ADAMTS9-CHL1 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.
ADAMTS9-CHL1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
ADAMTS9-CHL1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
ADAMTS9-CHL1 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
ADAMTS9-CHL1 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
HgeneADAMTS9

GO:0006508

proteolysis

12514189


check buttonFusion gene breakpoints across ADAMTS9 (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 CHL1 (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
ChimerDB4LUADTCGA-62-8395-01AADAMTS9chr3

64619374

-CHL1chr3

447178

+


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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)
ENST00000295903ADAMTS9chr364619374-ENST00000397491CHL1chr3447178+33341976222058678
ENST00000498707ADAMTS9chr364619374-ENST00000397491CHL1chr3447178+373923813432463706

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
ENST00000295903ENST00000397491ADAMTS9chr364619374-CHL1chr3447178+0.0015061270.9984939
ENST00000498707ENST00000397491ADAMTS9chr364619374-CHL1chr3447178+0.0015063830.99849355

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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

>2112_2112_1_ADAMTS9-CHL1_ADAMTS9_chr3_64619374_ENST00000295903_CHL1_chr3_447178_ENST00000397491_length(amino acids)=678AA_BP=652
MQFVSWATLLTLLVRDLAEMGSPDAAAAVRKDRLHPRQVKLLETLSEYEIVSPIRVNALGEPFPTNVHFKRTRRSINSATDPWPAFASSS
SSSTSSQAHYRLSAFGQQFLFNLTANAGFIAPLFTVTLLGTPGVNQTKFYSEEEAELKHCFYKGYVNTNSEHTAVISLCSGMLGTFRSHD
GDYFIEPLQSMDEQEDEEEQNKPHIIYRRSAPQREPSTGRHACDTSEHKNRHSKDKKKTRARKWGERINLAGDVAALNSGLATEAFSAYG
NKTDNTREKRTHRRTKRFLSYPRFVEVLVVADNRMVSYHGENLQHYILTLMSIDGPSISFNAQTTLKNFCQWQHSKNSPGGIHHDTAVLL
TRQDICRAHDKCDTLGLAELGTICDPYRSCSISEDSGLSTAFTIAHELGHVFNMPHDDNNKCKEEGVKSPQHVMAPTLNFYTNPWMWSKC
SRKYITEFLDTGYGECLLNEPESRPYPLPVQLPGILYNVNKQCELIFGPGSQVCPYMMQCRRLWCNNVNGVHKGCRTQHTPWADGTECEP
GKHCKYGFCVPKEMDVPVTDGSWGSWSPFGTCSRTCGGGIKTAIRECNRPEPKNGGKYCVGRRMKFKSCNTEPCLKQKRDFRDEQCAHFD

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

>2112_2112_2_ADAMTS9-CHL1_ADAMTS9_chr3_64619374_ENST00000498707_CHL1_chr3_447178_ENST00000397491_length(amino acids)=706AA_BP=680
MQFVSWATLLTLLVRDLAEMGSPDAAAAVRKDRLHPRQVKLLETLSEYEIVSPIRVNALGEPFPTNVHFKRTRRSINSATDPWPAFASSS
SSSTSSQAHYRLSAFGQQFLFNLTANAGFIAPLFTVTLLGTPGVNQTKFYSEEEAELKHCFYKGYVNTNSEHTAVISLCSGMLGTFRSHD
GDYFIEPLQSMDEQEDEEEQNKPHIIYRRSAPQREPSTGRHACDTSEHKNRHSKDKKKTRARKWGERINLAGDVAALNSGLATEAFSAYG
NKTDNTREKRTHRRTKRFLSYPRFVEVLVVADNRMVSYHGENLQHYILTLMSIVASIYKDPSIGNLINIVIVNLIVIHNEQDGPSISFNA
QTTLKNFCQWQHSKNSPGGIHHDTAVLLTRQDICRAHDKCDTLGLAELGTICDPYRSCSISEDSGLSTAFTIAHELGHVFNMPHDDNNKC
KEEGVKSPQHVMAPTLNFYTNPWMWSKCSRKYITEFLDTGYGECLLNEPESRPYPLPVQLPGILYNVNKQCELIFGPGSQVCPYMMQCRR
LWCNNVNGVHKGCRTQHTPWADGTECEPGKHCKYGFCVPKEMDVPVTDGSWGSWSPFGTCSRTCGGGIKTAIRECNRPEPKNGGKYCVGR

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

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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/chr3:64619374/chr3:447178)
- 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
ADAMTS9

Q9P2N4

CHL1

O00533

FUNCTION: Cleaves the large aggregating proteoglycans, aggrecan (at the '1838-Glu-|-Ala-1839' site) and versican (at the '1428-Glu-|-Ala-1429' site). Has a protease-independent function in promoting the transport from the endoplasmic reticulum to the Golgi apparatus of a variety of secretory cargos. {ECO:0000269|PubMed:12514189, ECO:0000269|PubMed:22419820}.FUNCTION: Extracellular matrix and cell adhesion protein that plays a role in nervous system development and in synaptic plasticity. Both soluble and membranous forms promote neurite outgrowth of cerebellar and hippocampal neurons and suppress neuronal cell death. Plays a role in neuronal positioning of pyramidal neurons and in regulation of both the number of interneurons and the efficacy of GABAergic synapses. May play a role in regulating cell migration in nerve regeneration and cortical development. Potentiates integrin-dependent cell migration towards extracellular matrix proteins. Recruits ANK3 to the plasma membrane (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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneADAMTS9chr3:64619374chr3:447178ENST00000295903-123988_96651.33333333333342196.6666666666665Compositional biasNote=Poly-Ser
HgeneADAMTS9chr3:64619374chr3:447178ENST00000498707-134088_96679.33333333333342117.3333333333335Compositional biasNote=Poly-Ser
HgeneADAMTS9chr3:64619374chr3:447178ENST00000295903-1239293_499651.33333333333342196.6666666666665DomainPeptidase M12B
HgeneADAMTS9chr3:64619374chr3:447178ENST00000295903-1239509_587651.33333333333342196.6666666666665DomainNote=Disintegrin
HgeneADAMTS9chr3:64619374chr3:447178ENST00000295903-1239588_643651.33333333333342196.6666666666665DomainTSP type-1 1
HgeneADAMTS9chr3:64619374chr3:447178ENST00000498707-1340293_499679.33333333333342117.3333333333335DomainPeptidase M12B
HgeneADAMTS9chr3:64619374chr3:447178ENST00000498707-1340509_587679.33333333333342117.3333333333335DomainNote=Disintegrin
HgeneADAMTS9chr3:64619374chr3:447178ENST00000498707-1340588_643679.33333333333342117.3333333333335DomainTSP type-1 1
HgeneADAMTS9chr3:64619374chr3:447178ENST00000295903-1239221_228651.33333333333342196.6666666666665MotifCysteine switch
HgeneADAMTS9chr3:64619374chr3:447178ENST00000498707-1340221_228679.33333333333342117.3333333333335MotifCysteine switch
TgeneCHL1chr3:64619374chr3:447178ENST0000025650926281181_11851152.66666666666671225.0MotifNote=FIG[AQ]Y
TgeneCHL1chr3:64619374chr3:447178ENST0000039749125271181_11851136.66666666666671209.0MotifNote=FIG[AQ]Y

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneADAMTS9chr3:64619374chr3:447178ENST00000295903-1239644_752651.33333333333342196.6666666666665Compositional biasNote=Cys-rich
HgeneADAMTS9chr3:64619374chr3:447178ENST00000498707-1340644_752679.33333333333342117.3333333333335Compositional biasNote=Cys-rich
HgeneADAMTS9chr3:64619374chr3:447178ENST00000295903-12391052_1109651.33333333333342196.6666666666665DomainTSP type-1 5
HgeneADAMTS9chr3:64619374chr3:447178ENST00000295903-12391110_1166651.33333333333342196.6666666666665DomainTSP type-1 6
HgeneADAMTS9chr3:64619374chr3:447178ENST00000295903-12391182_1240651.33333333333342196.6666666666665DomainTSP type-1 7
HgeneADAMTS9chr3:64619374chr3:447178ENST00000295903-12391241_1296651.33333333333342196.6666666666665DomainTSP type-1 8
HgeneADAMTS9chr3:64619374chr3:447178ENST00000295903-12391328_1379651.33333333333342196.6666666666665DomainTSP type-1 9
HgeneADAMTS9chr3:64619374chr3:447178ENST00000295903-12391382_1440651.33333333333342196.6666666666665DomainTSP type-1 10
HgeneADAMTS9chr3:64619374chr3:447178ENST00000295903-12391441_1494651.33333333333342196.6666666666665DomainTSP type-1 11
HgeneADAMTS9chr3:64619374chr3:447178ENST00000295903-12391497_1555651.33333333333342196.6666666666665DomainTSP type-1 12
HgeneADAMTS9chr3:64619374chr3:447178ENST00000295903-12391556_1611651.33333333333342196.6666666666665DomainTSP type-1 13
HgeneADAMTS9chr3:64619374chr3:447178ENST00000295903-12391612_1676651.33333333333342196.6666666666665DomainTSP type-1 14
HgeneADAMTS9chr3:64619374chr3:447178ENST00000295903-12391677_1734651.33333333333342196.6666666666665DomainTSP type-1 15
HgeneADAMTS9chr3:64619374chr3:447178ENST00000295903-12391735_1935651.33333333333342196.6666666666665DomainGON
HgeneADAMTS9chr3:64619374chr3:447178ENST00000295903-1239878_936651.33333333333342196.6666666666665DomainTSP type-1 2
HgeneADAMTS9chr3:64619374chr3:447178ENST00000295903-1239939_997651.33333333333342196.6666666666665DomainTSP type-1 3
HgeneADAMTS9chr3:64619374chr3:447178ENST00000295903-1239998_1049651.33333333333342196.6666666666665DomainTSP type-1 4
HgeneADAMTS9chr3:64619374chr3:447178ENST00000498707-13401052_1109679.33333333333342117.3333333333335DomainTSP type-1 5
HgeneADAMTS9chr3:64619374chr3:447178ENST00000498707-13401110_1166679.33333333333342117.3333333333335DomainTSP type-1 6
HgeneADAMTS9chr3:64619374chr3:447178ENST00000498707-13401182_1240679.33333333333342117.3333333333335DomainTSP type-1 7
HgeneADAMTS9chr3:64619374chr3:447178ENST00000498707-13401241_1296679.33333333333342117.3333333333335DomainTSP type-1 8
HgeneADAMTS9chr3:64619374chr3:447178ENST00000498707-13401328_1379679.33333333333342117.3333333333335DomainTSP type-1 9
HgeneADAMTS9chr3:64619374chr3:447178ENST00000498707-13401382_1440679.33333333333342117.3333333333335DomainTSP type-1 10
HgeneADAMTS9chr3:64619374chr3:447178ENST00000498707-13401441_1494679.33333333333342117.3333333333335DomainTSP type-1 11
HgeneADAMTS9chr3:64619374chr3:447178ENST00000498707-13401497_1555679.33333333333342117.3333333333335DomainTSP type-1 12
HgeneADAMTS9chr3:64619374chr3:447178ENST00000498707-13401556_1611679.33333333333342117.3333333333335DomainTSP type-1 13
HgeneADAMTS9chr3:64619374chr3:447178ENST00000498707-13401612_1676679.33333333333342117.3333333333335DomainTSP type-1 14
HgeneADAMTS9chr3:64619374chr3:447178ENST00000498707-13401677_1734679.33333333333342117.3333333333335DomainTSP type-1 15
HgeneADAMTS9chr3:64619374chr3:447178ENST00000498707-13401735_1935679.33333333333342117.3333333333335DomainGON
HgeneADAMTS9chr3:64619374chr3:447178ENST00000498707-1340878_936679.33333333333342117.3333333333335DomainTSP type-1 2
HgeneADAMTS9chr3:64619374chr3:447178ENST00000498707-1340939_997679.33333333333342117.3333333333335DomainTSP type-1 3
HgeneADAMTS9chr3:64619374chr3:447178ENST00000498707-1340998_1049679.33333333333342117.3333333333335DomainTSP type-1 4
HgeneADAMTS9chr3:64619374chr3:447178ENST00000295903-1239753_877651.33333333333342196.6666666666665RegionNote=Spacer
HgeneADAMTS9chr3:64619374chr3:447178ENST00000498707-1340753_877679.33333333333342117.3333333333335RegionNote=Spacer
TgeneCHL1chr3:64619374chr3:447178ENST000002565092628128_2231152.66666666666671225.0DomainNote=Ig-like C2-type 2
TgeneCHL1chr3:64619374chr3:447178ENST000002565092628235_3281152.66666666666671225.0DomainNote=Ig-like C2-type 3
TgeneCHL1chr3:64619374chr3:447178ENST000002565092628331_4171152.66666666666671225.0DomainNote=Ig-like C2-type 4
TgeneCHL1chr3:64619374chr3:447178ENST00000256509262835_1241152.66666666666671225.0DomainNote=Ig-like C2-type 1
TgeneCHL1chr3:64619374chr3:447178ENST000002565092628423_5101152.66666666666671225.0DomainNote=Ig-like C2-type 5
TgeneCHL1chr3:64619374chr3:447178ENST000002565092628515_6071152.66666666666671225.0DomainNote=Ig-like C2-type 6
TgeneCHL1chr3:64619374chr3:447178ENST000002565092628614_7091152.66666666666671225.0DomainFibronectin type-III 1
TgeneCHL1chr3:64619374chr3:447178ENST000002565092628714_8071152.66666666666671225.0DomainFibronectin type-III 2
TgeneCHL1chr3:64619374chr3:447178ENST000002565092628809_9141152.66666666666671225.0DomainFibronectin type-III 3
TgeneCHL1chr3:64619374chr3:447178ENST000002565092628918_10151152.66666666666671225.0DomainFibronectin type-III 4
TgeneCHL1chr3:64619374chr3:447178ENST000003974912527128_2231136.66666666666671209.0DomainNote=Ig-like C2-type 2
TgeneCHL1chr3:64619374chr3:447178ENST000003974912527235_3281136.66666666666671209.0DomainNote=Ig-like C2-type 3
TgeneCHL1chr3:64619374chr3:447178ENST000003974912527331_4171136.66666666666671209.0DomainNote=Ig-like C2-type 4
TgeneCHL1chr3:64619374chr3:447178ENST00000397491252735_1241136.66666666666671209.0DomainNote=Ig-like C2-type 1
TgeneCHL1chr3:64619374chr3:447178ENST000003974912527423_5101136.66666666666671209.0DomainNote=Ig-like C2-type 5
TgeneCHL1chr3:64619374chr3:447178ENST000003974912527515_6071136.66666666666671209.0DomainNote=Ig-like C2-type 6
TgeneCHL1chr3:64619374chr3:447178ENST000003974912527614_7091136.66666666666671209.0DomainFibronectin type-III 1
TgeneCHL1chr3:64619374chr3:447178ENST000003974912527714_8071136.66666666666671209.0DomainFibronectin type-III 2
TgeneCHL1chr3:64619374chr3:447178ENST000003974912527809_9141136.66666666666671209.0DomainFibronectin type-III 3
TgeneCHL1chr3:64619374chr3:447178ENST000003974912527918_10151136.66666666666671209.0DomainFibronectin type-III 4
TgeneCHL1chr3:64619374chr3:447178ENST000002565092628555_5581152.66666666666671225.0MotifNote=DGEA
TgeneCHL1chr3:64619374chr3:447178ENST000003974912527555_5581136.66666666666671209.0MotifNote=DGEA
TgeneCHL1chr3:64619374chr3:447178ENST0000025650926281104_12081152.66666666666671225.0Topological domainCytoplasmic
TgeneCHL1chr3:64619374chr3:447178ENST00000256509262825_10821152.66666666666671225.0Topological domainExtracellular
TgeneCHL1chr3:64619374chr3:447178ENST0000039749125271104_12081136.66666666666671209.0Topological domainCytoplasmic
TgeneCHL1chr3:64619374chr3:447178ENST00000397491252725_10821136.66666666666671209.0Topological domainExtracellular
TgeneCHL1chr3:64619374chr3:447178ENST0000025650926281083_11031152.66666666666671225.0TransmembraneHelical
TgeneCHL1chr3:64619374chr3:447178ENST0000039749125271083_11031136.66666666666671209.0TransmembraneHelical


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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
ADAMTS9
CHL1


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 ADAMTS9-CHL1


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 ADAMTS9-CHL1


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