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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 26618

FusionGeneSummary for PDZRN3_TMC1

check button Fusion gene summary
Fusion gene informationFusion gene name: PDZRN3_TMC1
Fusion gene ID: 26618
HgeneTgene
Gene symbol

PDZRN3

TMC1

Gene ID

23024

117531

Gene namePDZ domain containing ring finger 3transmembrane channel like 1
SynonymsLNX3|SEMACAP3|SEMCAP3DFNA36|DFNB11|DFNB7
Cytomap

3p13

9q21.13

Type of geneprotein-codingprotein-coding
DescriptionE3 ubiquitin-protein ligase PDZRN3RING-type E3 ubiquitin transferase PDZRN3ligand of Numb protein X 3likely ortholog of mouse semaF cytoplasmic domain associated protein 3semaphorin cytoplasmic domain-associated protein 3transmembrane channel-like protein 1transmembrane cochlear-expressed protein 1transmembrane, cochlear expressed, 1
Modification date2018052320180523
UniProtAcc

Q9UPQ7

Q8TDI8

Ensembl transtripts involved in fusion geneENST00000263666, ENST00000466780, 
ENST00000308537, ENST00000462146, 
ENST00000535920, ENST00000479530, 
ENST00000466348, 
ENST00000297784, 
ENST00000340019, ENST00000396237, 
ENST00000486417, 
Fusion gene scores* DoF score8 X 4 X 6=1923 X 3 X 3=27
# samples 103
** MAII scorelog2(10/192*10)=-0.941106310946431
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: PDZRN3 [Title/Abstract] AND TMC1 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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 button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVLGGTCGA-HT-7476-01APDZRN3chr3

73651505

-TMC1chr9

75403255

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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-shitENST00000263666ENST00000297784PDZRN3chr3

73651505

-TMC1chr9

75403255

+
Frame-shitENST00000263666ENST00000340019PDZRN3chr3

73651505

-TMC1chr9

75403255

+
Frame-shitENST00000263666ENST00000396237PDZRN3chr3

73651505

-TMC1chr9

75403255

+
5CDS-intronENST00000263666ENST00000486417PDZRN3chr3

73651505

-TMC1chr9

75403255

+
intron-3CDSENST00000466780ENST00000297784PDZRN3chr3

73651505

-TMC1chr9

75403255

+
intron-3CDSENST00000466780ENST00000340019PDZRN3chr3

73651505

-TMC1chr9

75403255

+
intron-3CDSENST00000466780ENST00000396237PDZRN3chr3

73651505

-TMC1chr9

75403255

+
intron-intronENST00000466780ENST00000486417PDZRN3chr3

73651505

-TMC1chr9

75403255

+
Frame-shitENST00000308537ENST00000297784PDZRN3chr3

73651505

-TMC1chr9

75403255

+
Frame-shitENST00000308537ENST00000340019PDZRN3chr3

73651505

-TMC1chr9

75403255

+
Frame-shitENST00000308537ENST00000396237PDZRN3chr3

73651505

-TMC1chr9

75403255

+
5CDS-intronENST00000308537ENST00000486417PDZRN3chr3

73651505

-TMC1chr9

75403255

+
intron-3CDSENST00000462146ENST00000297784PDZRN3chr3

73651505

-TMC1chr9

75403255

+
intron-3CDSENST00000462146ENST00000340019PDZRN3chr3

73651505

-TMC1chr9

75403255

+
intron-3CDSENST00000462146ENST00000396237PDZRN3chr3

73651505

-TMC1chr9

75403255

+
intron-intronENST00000462146ENST00000486417PDZRN3chr3

73651505

-TMC1chr9

75403255

+
intron-3CDSENST00000535920ENST00000297784PDZRN3chr3

73651505

-TMC1chr9

75403255

+
intron-3CDSENST00000535920ENST00000340019PDZRN3chr3

73651505

-TMC1chr9

75403255

+
intron-3CDSENST00000535920ENST00000396237PDZRN3chr3

73651505

-TMC1chr9

75403255

+
intron-intronENST00000535920ENST00000486417PDZRN3chr3

73651505

-TMC1chr9

75403255

+
intron-3CDSENST00000479530ENST00000297784PDZRN3chr3

73651505

-TMC1chr9

75403255

+
intron-3CDSENST00000479530ENST00000340019PDZRN3chr3

73651505

-TMC1chr9

75403255

+
intron-3CDSENST00000479530ENST00000396237PDZRN3chr3

73651505

-TMC1chr9

75403255

+
intron-intronENST00000479530ENST00000486417PDZRN3chr3

73651505

-TMC1chr9

75403255

+
intron-3CDSENST00000466348ENST00000297784PDZRN3chr3

73651505

-TMC1chr9

75403255

+
intron-3CDSENST00000466348ENST00000340019PDZRN3chr3

73651505

-TMC1chr9

75403255

+
intron-3CDSENST00000466348ENST00000396237PDZRN3chr3

73651505

-TMC1chr9

75403255

+
intron-intronENST00000466348ENST00000486417PDZRN3chr3

73651505

-TMC1chr9

75403255

+

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FusionProtFeatures for PDZRN3_TMC1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
PDZRN3

Q9UPQ7

TMC1

Q8TDI8

E3 ubiquitin-protein ligase. Plays an important role inregulating the surface level of MUSK on myotubes. Mediates theubiquitination of MUSK, promoting its endocytosis and lysosomaldegradation. Might contribute to terminal myogenicdifferentiation. {ECO:0000250|UniProtKB:Q69ZS0}. Probable ion channel required for the normal function ofcochlear hair cells. {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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FusionGeneSequence for PDZRN3_TMC1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for PDZRN3_TMC1


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
PDZRN3MUSK, UBE2D2, LNX1, LNX2, OIP5, FAM13C, OFD1, SDHA, ZNF785, STX11, POTEB3, FZD4TMC1COPS5, CAND1


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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RelatedDrugs for PDZRN3_TMC1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for PDZRN3_TMC1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePDZRN3C0023893Liver Cirrhosis, Experimental1CTD_human
TgeneTMC1C1832978Deafness, Autosomal Recessive 71CTD_human;UNIPROT
TgeneTMC1C1847626Deafness, Autosomal Dominant 361CTD_human;UNIPROT