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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: 41191

FusionGeneSummary for USP6NL_FRMD4A

check button Fusion gene summary
Fusion gene informationFusion gene name: USP6NL_FRMD4A
Fusion gene ID: 41191
HgeneTgene
Gene symbol

USP6NL

FRMD4A

Gene ID

9712

55691

Gene nameUSP6 N-terminal likeFERM domain containing 4A
SynonymsRNTRE|TRE2NL|USP6NL-IT1CCAFCA|FRMD4|bA295P9.4
Cytomap

10p14

10p13

Type of geneprotein-codingprotein-coding
DescriptionUSP6 N-terminal-like proteinrelated to the N-terminus of treFERM domain-containing protein 4AFERM domain containing 4
Modification date2018052320180519
UniProtAcc

Q92738

Q9P2Q2

Ensembl transtripts involved in fusion geneENST00000609104, ENST00000277575, 
ENST00000379237, ENST00000443016, 
ENST00000609853, 
ENST00000358621, 
ENST00000357447, ENST00000378503, 
ENST00000342409, ENST00000493380, 
ENST00000475141, ENST00000492155, 
Fusion gene scores* DoF score17 X 12 X 9=18369 X 7 X 6=378
# samples 1810
** MAII scorelog2(18/1836*10)=-3.35049724708413
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(10/378*10)=-1.91838623444635
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: USP6NL [Title/Abstract] AND FRMD4A [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
HgeneUSP6NL

GO:0043547

positive regulation of GTPase activity

17562788


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
TCGALDOVTCGA-13-1511-01AUSP6NLchr10

11639630

-FRMD4Achr10

13900912

-
* 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-shitENST00000609104ENST00000358621USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
Frame-shitENST00000609104ENST00000357447USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
Frame-shitENST00000609104ENST00000378503USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
Frame-shitENST00000609104ENST00000342409USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
5CDS-intronENST00000609104ENST00000493380USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
5CDS-intronENST00000609104ENST00000475141USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
5CDS-intronENST00000609104ENST00000492155USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-3CDSENST00000277575ENST00000358621USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-3CDSENST00000277575ENST00000357447USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-3CDSENST00000277575ENST00000378503USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-3CDSENST00000277575ENST00000342409USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-intronENST00000277575ENST00000493380USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-intronENST00000277575ENST00000475141USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-intronENST00000277575ENST00000492155USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-3CDSENST00000379237ENST00000358621USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-3CDSENST00000379237ENST00000357447USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-3CDSENST00000379237ENST00000378503USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-3CDSENST00000379237ENST00000342409USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-intronENST00000379237ENST00000493380USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-intronENST00000379237ENST00000475141USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-intronENST00000379237ENST00000492155USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-3CDSENST00000443016ENST00000358621USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-3CDSENST00000443016ENST00000357447USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-3CDSENST00000443016ENST00000378503USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-3CDSENST00000443016ENST00000342409USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-intronENST00000443016ENST00000493380USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-intronENST00000443016ENST00000475141USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-intronENST00000443016ENST00000492155USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-3CDSENST00000609853ENST00000358621USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-3CDSENST00000609853ENST00000357447USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-3CDSENST00000609853ENST00000378503USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-3CDSENST00000609853ENST00000342409USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-intronENST00000609853ENST00000493380USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-intronENST00000609853ENST00000475141USP6NLchr10

11639630

-FRMD4Achr10

13900912

-
intron-intronENST00000609853ENST00000492155USP6NLchr10

11639630

-FRMD4Achr10

13900912

-

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FusionProtFeatures for USP6NL_FRMD4A


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
USP6NL

Q92738

FRMD4A

Q9P2Q2

Acts as a GTPase-activating protein for RAB5A and RAB43.Involved in receptor trafficking. In complex with EPS8 inhibitsinternalization of EGFR. Involved in retrograde transport from theendocytic pathway to the Golgi apparatus. Involved in thetransport of Shiga toxin from early and recycling endosomes to thetrans-Golgi network. Required for structural integrity of theGolgi complex. {ECO:0000269|PubMed:11099046,ECO:0000269|PubMed:17562788, ECO:0000269|PubMed:17684057}. Scaffolding protein that regulates epithelial cellpolarity by connecting ARF6 activation with the PAR3 complex (Bysimilarity). Plays a redundant role with FRMD4B in epithelialpolarization (By similarity). May regulate MAPT secretion byactivating ARF6-signaling (PubMed:27044754).{ECO:0000250|UniProtKB:Q8BIE6, ECO:0000269|PubMed:27044754}.

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 USP6NL_FRMD4A


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 USP6NL_FRMD4A


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
USP6NLACTN4, GRB2, APP, WWOX, SHMT2, NXF1, TMEM17, CCNA2, COMT, ANAPC15, UBE2S, CDH1FRMD4AHNRNPA1, TRAF3IP1, YEATS4, WDR83


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 USP6NL_FRMD4A


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 USP6NL_FRMD4A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneUSP6NLC0025202melanoma1CTD_human
TgeneFRMD4AC0236969Substance-Related Disorders1CTD_human