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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: 20467

FusionGeneSummary for LYST_NID1

check button Fusion gene summary
Fusion gene informationFusion gene name: LYST_NID1
Fusion gene ID: 20467
HgeneTgene
Gene symbol

LYST

NID1

Gene ID

1130

4811

Gene namelysosomal trafficking regulatornidogen 1
SynonymsCHS|CHS1NID
Cytomap

1q42.3

1q42.3

Type of geneprotein-codingprotein-coding
Descriptionlysosomal-trafficking regulatorChediak-Higashi syndrome 1beige homolognidogen-1NID-1enactinentactin
Modification date2018051920180522
UniProtAcc

Q99698

P14543

Ensembl transtripts involved in fusion geneENST00000389794, ENST00000389793, 
ENST00000536965, ENST00000473037, 
ENST00000366595, ENST00000264187, 
Fusion gene scores* DoF score5 X 7 X 6=2103 X 5 X 4=60
# samples 75
** MAII scorelog2(7/210*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(5/60*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LYST [Title/Abstract] AND NID1 [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
TCGARVLUADTCGA-55-7576-01ALYSTchr1

235933460

-NID1chr1

236148805

-
TCGALDLUSCTCGA-43-7656-01ALYSTchr1

235976271

-NID1chr1

236175343

-
TCGARVSKCMTCGA-EE-A2MS-06ALYSTchr1

235950500

-NID1chr1

236212289

-
* 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-shiftENST00000389794ENST00000366595LYSTchr1

235933460

-NID1chr1

236148805

-
Frame-shiftENST00000389794ENST00000264187LYSTchr1

235933460

-NID1chr1

236148805

-
Frame-shiftENST00000389793ENST00000366595LYSTchr1

235933460

-NID1chr1

236148805

-
Frame-shiftENST00000389793ENST00000264187LYSTchr1

235933460

-NID1chr1

236148805

-
3UTR-3CDSENST00000536965ENST00000366595LYSTchr1

235933460

-NID1chr1

236148805

-
3UTR-3CDSENST00000536965ENST00000264187LYSTchr1

235933460

-NID1chr1

236148805

-
intron-3CDSENST00000473037ENST00000366595LYSTchr1

235933460

-NID1chr1

236148805

-
intron-3CDSENST00000473037ENST00000264187LYSTchr1

235933460

-NID1chr1

236148805

-
5CDS-intronENST00000389794ENST00000366595LYSTchr1

235976271

-NID1chr1

236175343

-
5CDS-intronENST00000389794ENST00000264187LYSTchr1

235976271

-NID1chr1

236175343

-
5CDS-intronENST00000389793ENST00000366595LYSTchr1

235976271

-NID1chr1

236175343

-
5CDS-intronENST00000389793ENST00000264187LYSTchr1

235976271

-NID1chr1

236175343

-
5CDS-intronENST00000536965ENST00000366595LYSTchr1

235976271

-NID1chr1

236175343

-
5CDS-intronENST00000536965ENST00000264187LYSTchr1

235976271

-NID1chr1

236175343

-
intron-intronENST00000473037ENST00000366595LYSTchr1

235976271

-NID1chr1

236175343

-
intron-intronENST00000473037ENST00000264187LYSTchr1

235976271

-NID1chr1

236175343

-
Frame-shiftENST00000389794ENST00000366595LYSTchr1

235950500

-NID1chr1

236212289

-
Frame-shiftENST00000389794ENST00000264187LYSTchr1

235950500

-NID1chr1

236212289

-
Frame-shiftENST00000389793ENST00000366595LYSTchr1

235950500

-NID1chr1

236212289

-
Frame-shiftENST00000389793ENST00000264187LYSTchr1

235950500

-NID1chr1

236212289

-
3UTR-3CDSENST00000536965ENST00000366595LYSTchr1

235950500

-NID1chr1

236212289

-
3UTR-3CDSENST00000536965ENST00000264187LYSTchr1

235950500

-NID1chr1

236212289

-
intron-3CDSENST00000473037ENST00000366595LYSTchr1

235950500

-NID1chr1

236212289

-
intron-3CDSENST00000473037ENST00000264187LYSTchr1

235950500

-NID1chr1

236212289

-

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FusionProtFeatures for LYST_NID1


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

Q99698

NID1

P14543

May be required for sorting endosomal resident proteinsinto late multivesicular endosomes by a mechanism involvingmicrotubules. Sulfated glycoprotein widely distributed in basementmembranes and tightly associated with laminin. Also binds tocollagen IV and perlecan. It probably has a role in cell-extracellular matrix interactions.

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 LYST_NID1


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 LYST_NID1


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
LYSTYWHAQ, CSNK2B, TNNI3, HGS, YWHAB, ESRRA, KPNB1, MRPS31, DGCR14, NCDN, PCBP4, VTA1, DNAJC14, CNTROB, ATN1, EFS, MED12, HNRNPM, CENPJ, MRPL17, ZNF521, CELF4, YWHAZ, HNRNPH2, LLGL2, MLH1, PPIA, TACC1, DAP3, MYH13, SAP30, KIF1C, GAR1, KLC3NID1LAMC1, COL4A1, COL1A1, LACRT, FBLN1, MDK, FGA, FGB, NID1, PTPRF, FBLN2, SKIL, DEFA5, LGALS9, PSG1, TAZ


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 LYST_NID1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneNID1P14543DB00013UrokinaseNidogen-1biotechapproved|investigational|withdrawn

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RelatedDiseases for LYST_NID1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneLYSTC0007965Chediak-Higashi Syndrome2CTD_human;ORPHANET;UNIPROT
TgeneNID1C0023893Liver Cirrhosis, Experimental1CTD_human
TgeneNID1C0043094Weight Gain1CTD_human