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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: 40967

FusionGeneSummary for USP12_LNX2

check button Fusion gene summary
Fusion gene informationFusion gene name: USP12_LNX2
Fusion gene ID: 40967
HgeneTgene
Gene symbol

USP12

LNX2

Gene ID

219333

222484

Gene nameubiquitin specific peptidase 12ligand of numb-protein X 2
SynonymsUBH1|USP12L1PDZRN1
Cytomap

13q12.13

13q12.2

Type of geneprotein-codingprotein-coding
Descriptionubiquitin carboxyl-terminal hydrolase 12deubiquitinating enzyme 12ubiquitin specific protease 12 like 1ubiquitin thioesterase 12ubiquitin thiolesterase 12ubiquitin-hydrolyzing enzyme 1ubiquitin-specific-processing protease 12ligand of Numb protein X 2PDZ domain containing ring finger 1PDZ domain-containing RING finger protein 1numb-binding protein 2
Modification date2018051920180519
UniProtAcc

O75317

Q8N448

Ensembl transtripts involved in fusion geneENST00000282344, ENST00000316334, 
Fusion gene scores* DoF score5 X 3 X 5=751 X 1 X 1=1
# samples 51
** MAII scorelog2(5/75*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(1/1*10)=3.32192809488736
Context

PubMed: USP12 [Title/Abstract] AND LNX2 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotationTumor suppressor gene involved fusion gene, in-frame but not retained their domain.
* 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
HgeneUSP12

GO:0016579

protein deubiquitination

19075014|24145035


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
TCGARVSTADTCGA-BR-4357-01AUSP12chr13

27669738

-LNX2chr13

28134122

-
* 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
In-frameENST00000282344ENST00000316334USP12chr13

27669738

-LNX2chr13

28134122

-

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FusionProtFeatures for USP12_LNX2


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
USP12

O75317

LNX2

Q8N448

Deubiquitinating enzyme. Has almost no deubiquitinatingactivity by itself and requires the interaction with WDR20 andWDR48 to have a high activity (PubMed:19075014, PubMed:27373336).Not involved in deubiquitination of monoubiquitinated FANCD2(PubMed:19075014). In complex with WDR48, acts as a potentialtumor suppressor by positively regulating PHLPP1 stability(PubMed:24145035). {ECO:0000269|PubMed:19075014,ECO:0000269|PubMed:24145035, ECO:0000269|PubMed:27373336}.

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
TgeneLNX2chr13:27669738chr13:28134122ENST00000316334-410468_554408691DomainPDZ 3
TgeneLNX2chr13:27669738chr13:28134122ENST00000316334-410600_688408691DomainPDZ 4

- In-frame and not-retained protein feature among the 13 regional features.
>
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneUSP12chr13:27669738chr13:28134122ENST00000282344-4939_369191371DomainNote=USP
TgeneLNX2chr13:27669738chr13:28134122ENST00000316334-410233_318408691DomainPDZ 1
TgeneLNX2chr13:27669738chr13:28134122ENST00000316334-410339_422408691DomainPDZ 2
TgeneLNX2chr13:27669738chr13:28134122ENST00000316334-410208_211408691MotifNote=NPXY motif
TgeneLNX2chr13:27669738chr13:28134122ENST00000316334-41050_88408691Zinc fingerRING-type


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FusionGeneSequence for USP12_LNX2


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.
>In-frame_USP12_ENST00000282344_chr13_27669738_-_LNX2_ENST00000316334_chr13_28134122_-_474aa
MEILMTVSKFASICTMGANASALEKEIGPEQFPVNEHYFGLVNFGNTCYCNSVLQALYFCRPFREKVLAYKSQPRKKESLLTCLADLFHS
IATQKKKVGVIPPKKFITRLRKENELFDNYMQQDAHEFLNYLLNTIADILQEERKQEKQNGRLPNGNIDNENNNSTPDPTWVHEIFQGTL
TNETRCLTCETASGERVNLTIARPGKPQPGNTIREAGNHSSSSQHHTPPPYYSRPSSHKDLTQCVTCQEKHITVKKEPHESLGMTVAGGR
GSKSGELPIFVTSVPPHGCLARDGRIKRGDVLLNINGIDLTNLSHSEAVAMLKASAASPAVALKALEVQIVEEATQNAEEQPSTFSENEY
DASWSPSWVMWLGLPSTLHSCHDIVLRRSYLGSWGFSIVGGYEENHTNQPFFIKTIVLGTPAYYDGRLKCGDMIVAVNGLSTVGMSHSAL


* Fusion transcript sequences (only coding sequence (CDS) region).
>In-frame_USP12_ENST00000282344_chr13_27669738_-_LNX2_ENST00000316334_chr13_28134122_-_1422nt
ATGGAAATCCTAATGACAGTCTCCAAATTCGCCTCCATCTGTACCATGGGCGCCAATGCTTCGGCATTAGAGAAAGAGATTGGTCCAGAA
CAGTTTCCGGTCAATGAGCACTATTTTGGATTAGTCAATTTTGGGAATACCTGCTACTGCAATTCAGTTCTTCAAGCACTTTATTTTTGT
CGTCCATTTCGGGAAAAAGTTCTTGCGTATAAGAGTCAACCTAGGAAAAAGGAGAGCCTTCTTACATGCTTAGCAGATCTCTTCCATAGC
ATAGCCACTCAGAAGAAAAAGGTTGGAGTAATACCCCCTAAGAAGTTCATCACAAGATTACGGAAAGAAAATGAGCTTTTTGACAACTAC
ATGCAACAAGATGCCCATGAATTCTTAAATTACCTACTAAATACAATTGCTGATATTTTACAAGAAGAGAGAAAGCAGGAAAAACAAAAT
GGTCGTTTACCTAATGGTAATATTGATAATGAAAATAATAACAGCACACCAGACCCAACGTGGGTTCATGAGATTTTTCAGGGAACATTA
ACTAATGAAACCAGATGTCTTACTTGTGAAACTGCCAGTGGAGAGAGAGTGAATTTAACAATTGCTAGACCAGGGAAACCCCAGCCTGGT
AACACCATTAGAGAAGCAGGAAATCATAGCAGCAGCAGCCAGCACCACACACCACCACCGTATTATAGCAGACCAAGCTCACATAAGGAT
CTTACTCAGTGTGTTACATGCCAAGAAAAACACATTACTGTAAAGAAGGAACCACATGAATCCCTTGGCATGACCGTTGCTGGGGGCAGG
GGAAGTAAGAGTGGTGAGCTGCCCATCTTTGTGACCAGTGTGCCACCCCATGGCTGCCTTGCACGAGATGGCAGAATAAAGAGAGGTGAT
GTGTTGCTAAATATCAACGGCATTGATTTGACCAATTTAAGTCACAGTGAGGCAGTTGCAATGCTGAAAGCCAGTGCCGCGTCCCCTGCT
GTTGCCCTTAAAGCACTTGAGGTCCAGATTGTTGAGGAGGCGACTCAGAACGCGGAGGAGCAGCCGAGTACTTTCAGCGAAAATGAGTAT
GATGCCAGTTGGTCCCCATCATGGGTCATGTGGCTTGGGCTTCCCAGCACACTTCATAGCTGCCACGATATAGTTTTACGAAGAAGTTAC
TTGGGAAGTTGGGGCTTTAGTATCGTTGGTGGATATGAAGAGAACCACACCAATCAGCCTTTTTTCATTAAAACTATTGTCTTGGGAACT
CCTGCTTATTATGATGGAAGATTAAAGTGTGGTGACATGATTGTGGCCGTAAATGGGCTGTCAACCGTGGGCATGAGCCACTCTGCACTA


* Fusion transcript sequences (Full-length transcript).
>In-frame_USP12_ENST00000282344_chr13_27669738_-_LNX2_ENST00000316334_chr13_28134122_-_4101nt
CGGAGGCAGCGGCTGCGCCCTGCGCCGGGGCGGAGCCGGGGGCGGGCCGGCGGCCGGCAGGCGGGGGCTGGGGCCCGAGGCCGGGAGTGC
CTGAGCGCCGGCGGCGACGACGGCAGCGGCGGCCCAGCGGGCTCGGTGGTTGGGTCCGCGGCGGCTCGGGGTCCGCCCGCGGGCTGCGGT
GCGAGCGGGCGGCCCGGCTCCCCTCCTCCCCCGCCCGCCGCCGCCGCTGTGATTGGGTGGAAGATGGCGCTGGCCGGATGGAAATCCTAA
TGACAGTCTCCAAATTCGCCTCCATCTGTACCATGGGCGCCAATGCTTCGGCATTAGAGAAAGAGATTGGTCCAGAACAGTTTCCGGTCA
ATGAGCACTATTTTGGATTAGTCAATTTTGGGAATACCTGCTACTGCAATTCAGTTCTTCAAGCACTTTATTTTTGTCGTCCATTTCGGG
AAAAAGTTCTTGCGTATAAGAGTCAACCTAGGAAAAAGGAGAGCCTTCTTACATGCTTAGCAGATCTCTTCCATAGCATAGCCACTCAGA
AGAAAAAGGTTGGAGTAATACCCCCTAAGAAGTTCATCACAAGATTACGGAAAGAAAATGAGCTTTTTGACAACTACATGCAACAAGATG
CCCATGAATTCTTAAATTACCTACTAAATACAATTGCTGATATTTTACAAGAAGAGAGAAAGCAGGAAAAACAAAATGGTCGTTTACCTA
ATGGTAATATTGATAATGAAAATAATAACAGCACACCAGACCCAACGTGGGTTCATGAGATTTTTCAGGGAACATTAACTAATGAAACCA
GATGTCTTACTTGTGAAACTGCCAGTGGAGAGAGAGTGAATTTAACAATTGCTAGACCAGGGAAACCCCAGCCTGGTAACACCATTAGAG
AAGCAGGAAATCATAGCAGCAGCAGCCAGCACCACACACCACCACCGTATTATAGCAGACCAAGCTCACATAAGGATCTTACTCAGTGTG
TTACATGCCAAGAAAAACACATTACTGTAAAGAAGGAACCACATGAATCCCTTGGCATGACCGTTGCTGGGGGCAGGGGAAGTAAGAGTG
GTGAGCTGCCCATCTTTGTGACCAGTGTGCCACCCCATGGCTGCCTTGCACGAGATGGCAGAATAAAGAGAGGTGATGTGTTGCTAAATA
TCAACGGCATTGATTTGACCAATTTAAGTCACAGTGAGGCAGTTGCAATGCTGAAAGCCAGTGCCGCGTCCCCTGCTGTTGCCCTTAAAG
CACTTGAGGTCCAGATTGTTGAGGAGGCGACTCAGAACGCGGAGGAGCAGCCGAGTACTTTCAGCGAAAATGAGTATGATGCCAGTTGGT
CCCCATCATGGGTCATGTGGCTTGGGCTTCCCAGCACACTTCATAGCTGCCACGATATAGTTTTACGAAGAAGTTACTTGGGAAGTTGGG
GCTTTAGTATCGTTGGTGGATATGAAGAGAACCACACCAATCAGCCTTTTTTCATTAAAACTATTGTCTTGGGAACTCCTGCTTATTATG
ATGGAAGATTAAAGTGTGGTGACATGATTGTGGCCGTAAATGGGCTGTCAACCGTGGGCATGAGCCACTCTGCACTAGTTCCCATGTTGA
AGGAGCAGAGGAACAAAGTCACTCTGACCGTTATTTGTTGGCCTGGCAGCCTTGTATAGATTTTGGAAATTGGTTTCAAATCTTGCATCT
TCCTTTTTTAGATTTTTGAAAGAAAACCCTTTGGTTTCATTGTGTTTGTGGTTTAGGAGCTGCTGACACTGCTGGTATACACAGGGCCAA
AACCCACTAAGATTGTCCGTTTATGTTTATTTAAATGGTTTCCTAAGTTAGTTACATTTCTTTTAGCTTGGAAACAGTCTTCCACTAACC
TTTGTGAGTTTATATTTTCAGAATTCAGACTTAGTTGTTAAAATGTTACCTATGGTAATGAGCAAAGCTCACCCAAACTGTGCCCCAGAT
GGAGTAAAGACCTTCTGGTGGGTCTTTGTTTTCAGTAACTGAATCATAGAACGAGTTCTGTATCCCTCAGGCCTGATGTCAGCAAAGCCA
GTAACAACAGCGTGTACTGCCACTGTCATAACCAATACCATGAATGAATATACTTTAAATTTTGGTGATAACTGTTCCCCATTTTTTTTT
GAACCACAGTCTCACTCTCACCCAGGCTGGAGTGCAGTGGCACAATCTCAGCTCACTGCAAGCTCCGCCTCCTGGGTTCACGCCATTCTC
CCACCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGTGTGCCACCATGCCCAGCTAATTTTTTGTACTTTTAGTAGAGACGGGGTTTCAC
CGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTTGTGATCTGCCCGCCTCAGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCTGCCG
CACCCGGCCGTTCCCATTTTTTATTGGTGCCAACATTTCAAAACTTCATACTGTTTATAAACTGATTTTCTGGTTTATTTCTACTGTAAT
CTCTCAATATTCATAGAAGATGAAGAAATAAGTCTGACAACACTAAAGAAATTTCTTAATATACTATTATTAGAATAGTAGAGGATAAAA
GATAATGTTATCCAGTTACAAAGGAATTTGGATGATAATTATAACTTAATGTTAGAGATGGTAAAGCTGCACTTACTTGAACAGCCCAAA
AGCATTAAAAATCTATTTCCAGAGGAATGTTTTGCTATGTAGGGAAATTTTGAAGTAGTTTTTGCTAAAAAATTATTTCTAGAGTTGTGT
TATTCTTAGCAGTAATCTTGGCTAGAAATGTTTTTGTGATTTATGCGATTAAACGAAATGATAAAGATAAAACCATATTATTAAATACCT
ATATATCACAGCTAAGTAGGAGAAAGGGAGACCTTTTTATTTTGTTCAGGTAGGAGTATTTCTTGTGTATTTTAGAAACAATTATTTTTC
CCATTATTTCTTATGAGATTAGTTGTTTCAAGTAGGAGACAGAAAAGTTCTGTTTTGTTGGAAATGTAGGTTTTAGATGTATCTTTCAGT
CAGCTCTCAGTCACTAGACTATTTCATATTTTTTGAAATGTTTTTGAAAATTATGACTAGCCCATTTTTTGTCCTTTATTCAACATACTT
ATCCTCTGAACACATAAATAAGTGAATAAGATAAAAATATCTTTACCTTATTAATATTATACATACTTGAAAAAAATTTCATTTAGAAAC
CTAGTTCAGAATCTGAGCAAATTTACAAGTGACCTCTGTAATAAATGGTATTGATAATCAGAGAATGTATTTCAGAATACTACAGTACAA
TATATTATGAAGCATGACCACTTTATTTTGAAACTTAGCAATTGTATTGCTGGGGTTTATTGTATCTGTAGCATGTCACTGATTATTTCA
GTTAGTTTTATAATGATTTTTAAAAAACATATCTATTTGGAATAAGATACAGCAACAATCATTGCTACTGACTTGTTCAACCCCTTAGTT
ACACTGTATGATCAACATATAACAAGATACAGTGGAATGGCCCATACAGTATATTACTGTTGTGTGATGATTGGCTTTGGAAGCAGTTTG
ATTTTGAAATGCTTTGATATTCTAATTGACATGGAACAAGTTTTTTCCCTGCTCCCCAAATAGAATTTTGTAACCAACTTTGCTATTTTT
TTAAAGTTTGTAAGAATGTGTCATTTCTTGGGGAGTAGCCATCCATCAACAAATATCCTGACTGCTACTTTGTTATATACAAAATACTTA
CATTGAACCTGGTGGCATAATGAGTATTTTGAAAGAAGAAATTTCTTCACTCTCATTTTTATAGAAATCTTGGAATCAGCTTAAGCTGTA
GCTTTTATGACAAAAGACAGTCATTTTTGGTCAGAGTGATATTTGGTGACGGAAACTTGTTCATAATTTATTGTTACTATAGAACTATTT
GGATTTTCTCATTTTTAGTTCTGATAGTTAAATATTTTGGTTTGTTCTGTGCCTTCAGTTTAAATTATTTCAGGATTTTTCAGATGTTTA


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FusionGenePPI for USP12_LNX2


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
USP12DHX8, DMWD, MMP2, PAIP1, RAD51AP1, USP39, PHLPP2, PHLPP1, NUP160, SDF4, UCHL5, WDR48, WDR20, USP46, HIST2H2AC, WDR26, WDR77, HIST2H2BE, ITCH, APP, AR, UBC, NOTCH1, VSX2, CBLB, ZAP70, LAT, GRB2, TRAT1, TSPYL6, GORASP1, RNF19B, GPR161, VSX1, HSPB9LNX2UBE2Z, UBE2I, UBE2T, CD8A, PRKCA, PLEKHG5, LNX1, CXADR, PKDREJ, PDZRN3, PDZRN4, MDGA1, CBX4, SHISA2, USP2, RLIM, RNF138, LATS2, IGSF5, LNX2, NXF1, NUMB, OPTN, TUBB, PEG10, MSRB3, MYLIP, IL16, ATP5B, NMD3, IP6K2, SCLY, PTCD3, MAPK9, MAP2K5, TRAF2, VTN, DDA1, C10orf88, LRRC8E, RBM17, PHYKPL, PIK3R3, SRSF11, UBE2D2, TRIM25, NOTCH1, SMARCB1


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 USP12_LNX2


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 USP12_LNX2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource