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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: 41193

FusionGeneSummary for USP6NL_GPHN

check button Fusion gene summary
Fusion gene informationFusion gene name: USP6NL_GPHN
Fusion gene ID: 41193
HgeneTgene
Gene symbol

USP6NL

GPHN

Gene ID

9712

10243

Gene nameUSP6 N-terminal likegephyrin
SynonymsRNTRE|TRE2NL|USP6NL-IT1GEPH|GPH|GPHRYN|HKPX1|MOCODC
Cytomap

10p14

14q23.3-q24.1

Type of geneprotein-codingprotein-coding
DescriptionUSP6 N-terminal-like proteinrelated to the N-terminus of tregephyrin
Modification date2018052320180523
UniProtAcc

Q92738

Q9NQX3

Ensembl transtripts involved in fusion geneENST00000609104, ENST00000277575, 
ENST00000379237, ENST00000443016, 
ENST00000609853, 		ENST00000315266, 
ENST00000478722, ENST00000459628, 
ENST00000543237, ENST00000305960, 
ENST00000544752, 
Fusion gene scores* DoF score17 X 12 X 9=18369 X 13 X 12=1404
# samples 1820
** MAII scorelog2(18/1836*10)=-3.35049724708413
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(20/1404*10)=-2.81147103052984
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: USP6NL [Title/Abstract] AND GPHN [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

TgeneGPHN

GO:0032324

molybdopterin cofactor biosynthetic process

26613940

TgeneGPHN

GO:0097112

gamma-aminobutyric acid receptor clustering

26613940


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
ChiTaRS3.1DB087988USP6NLchr10

11639629

-GPHNchr14

67291192

+
* 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-shiftENST00000609104ENST00000315266USP6NLchr10

11639629

-GPHNchr14

67291192

+
Frame-shiftENST00000609104ENST00000478722USP6NLchr10

11639629

-GPHNchr14

67291192

+
5CDS-intronENST00000609104ENST00000459628USP6NLchr10

11639629

-GPHNchr14

67291192

+
5CDS-intronENST00000609104ENST00000543237USP6NLchr10

11639629

-GPHNchr14

67291192

+
5CDS-intronENST00000609104ENST00000305960USP6NLchr10

11639629

-GPHNchr14

67291192

+
5CDS-3UTRENST00000609104ENST00000544752USP6NLchr10

11639629

-GPHNchr14

67291192

+
intron-3CDSENST00000277575ENST00000315266USP6NLchr10

11639629

-GPHNchr14

67291192

+
intron-3CDSENST00000277575ENST00000478722USP6NLchr10

11639629

-GPHNchr14

67291192

+
intron-intronENST00000277575ENST00000459628USP6NLchr10

11639629

-GPHNchr14

67291192

+
intron-intronENST00000277575ENST00000543237USP6NLchr10

11639629

-GPHNchr14

67291192

+
intron-intronENST00000277575ENST00000305960USP6NLchr10

11639629

-GPHNchr14

67291192

+
intron-3UTRENST00000277575ENST00000544752USP6NLchr10

11639629

-GPHNchr14

67291192

+
intron-3CDSENST00000379237ENST00000315266USP6NLchr10

11639629

-GPHNchr14

67291192

+
intron-3CDSENST00000379237ENST00000478722USP6NLchr10

11639629

-GPHNchr14

67291192

+
intron-intronENST00000379237ENST00000459628USP6NLchr10

11639629

-GPHNchr14

67291192

+
intron-intronENST00000379237ENST00000543237USP6NLchr10

11639629

-GPHNchr14

67291192

+
intron-intronENST00000379237ENST00000305960USP6NLchr10

11639629

-GPHNchr14

67291192

+
intron-3UTRENST00000379237ENST00000544752USP6NLchr10

11639629

-GPHNchr14

67291192

+
intron-3CDSENST00000443016ENST00000315266USP6NLchr10

11639629

-GPHNchr14

67291192

+
intron-3CDSENST00000443016ENST00000478722USP6NLchr10

11639629

-GPHNchr14

67291192

+
intron-intronENST00000443016ENST00000459628USP6NLchr10

11639629

-GPHNchr14

67291192

+
intron-intronENST00000443016ENST00000543237USP6NLchr10

11639629

-GPHNchr14

67291192

+
intron-intronENST00000443016ENST00000305960USP6NLchr10

11639629

-GPHNchr14

67291192

+
intron-3UTRENST00000443016ENST00000544752USP6NLchr10

11639629

-GPHNchr14

67291192

+
intron-3CDSENST00000609853ENST00000315266USP6NLchr10

11639629

-GPHNchr14

67291192

+
intron-3CDSENST00000609853ENST00000478722USP6NLchr10

11639629

-GPHNchr14

67291192

+
intron-intronENST00000609853ENST00000459628USP6NLchr10

11639629

-GPHNchr14

67291192

+
intron-intronENST00000609853ENST00000543237USP6NLchr10

11639629

-GPHNchr14

67291192

+
intron-intronENST00000609853ENST00000305960USP6NLchr10

11639629

-GPHNchr14

67291192

+
intron-3UTRENST00000609853ENST00000544752USP6NLchr10

11639629

-GPHNchr14

67291192

+

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FusionProtFeatures for USP6NL_GPHN


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

Q92738

GPHN

Q9NQX3

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}. Microtubule-associated protein involved in membraneprotein-cytoskeleton interactions. It is thought to anchor theinhibitory glycine receptor (GLYR) to subsynaptic microtubules.Catalyzes two steps in the biosynthesis of the molybdenumcofactor. In the first step, molybdopterin is adenylated.Subsequently, molybdate is inserted into adenylated molybdopterinand AMP is released. {ECO:0000269|PubMed:26613940}.

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_GPHN


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_GPHN


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, CDH1GPHNARHGEF9, GLRB, MTOR, PFN1, OTUD4, PRPF4, PCK1, SPATS1, GPHN, KHDRBS1, ACADVL, BRCC3, MTA2, PAAF1, PPP4R1, ROCK2, SPTAN1, TSSK1B, ODF3L2, NTRK1, DYNLL1, CDCA5, TCF4, SENP3, VASP, ENAH, KLKB1, KMO, LGALS3BP, STS, DYNLL2


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_GPHN


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_GPHN


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneUSP6NLC0025202melanoma1CTD_human
TgeneGPHNC0001973Alcoholic Intoxication, Chronic1CTD_human
TgeneGPHNC0236736Cocaine-Related Disorders1CTD_human
TgeneGPHNC1854990Molybdenum Cofactor Deficiency, Complementation Group C1ORPHANET;UNIPROT