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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: 20439

FusionGeneSummary for LYAR_COL6A3

check button Fusion gene summary
Fusion gene informationFusion gene name: LYAR_COL6A3
Fusion gene ID: 20439
HgeneTgene
Gene symbol

LYAR

COL6A3

Gene ID

55646

1293

Gene nameLy1 antibody reactivecollagen type VI alpha 3 chain
SynonymsZC2HC2|ZLYARBTHLM1|DYT27|UCMD1
Cytomap

4p16.3

2q37.3

Type of geneprotein-codingprotein-coding
Descriptioncell growth-regulating nucleolar proteinLy1 antibody reactive homologcollagen alpha-3(VI) chaincollagen VI, alpha-3 polypeptidecollagen, type VI, alpha 3
Modification date2018051920180523
UniProtAcc

Q9NX58

P12111

Ensembl transtripts involved in fusion geneENST00000343470, ENST00000452476, 
ENST00000347401, ENST00000353578, 
ENST00000295550, ENST00000472056, 
ENST00000409809, ENST00000346358, 
ENST00000392004, ENST00000392003, 
ENST00000473258, 
Fusion gene scores* DoF score4 X 4 X 2=328 X 8 X 2=128
# samples 48
** MAII scorelog2(4/32*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(8/128*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LYAR [Title/Abstract] AND COL6A3 [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
ChiTaRS3.1BU616556LYARchr4

4283622

+COL6A3chr2

238275370

+
* 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
intron-3CDSENST00000343470ENST00000347401LYARchr4

4283622

+COL6A3chr2

238275370

+
intron-3CDSENST00000343470ENST00000353578LYARchr4

4283622

+COL6A3chr2

238275370

+
intron-3CDSENST00000343470ENST00000295550LYARchr4

4283622

+COL6A3chr2

238275370

+
intron-3CDSENST00000343470ENST00000472056LYARchr4

4283622

+COL6A3chr2

238275370

+
intron-3CDSENST00000343470ENST00000409809LYARchr4

4283622

+COL6A3chr2

238275370

+
intron-3CDSENST00000343470ENST00000346358LYARchr4

4283622

+COL6A3chr2

238275370

+
intron-intronENST00000343470ENST00000392004LYARchr4

4283622

+COL6A3chr2

238275370

+
intron-intronENST00000343470ENST00000392003LYARchr4

4283622

+COL6A3chr2

238275370

+
intron-intronENST00000343470ENST00000473258LYARchr4

4283622

+COL6A3chr2

238275370

+
intron-3CDSENST00000452476ENST00000347401LYARchr4

4283622

+COL6A3chr2

238275370

+
intron-3CDSENST00000452476ENST00000353578LYARchr4

4283622

+COL6A3chr2

238275370

+
intron-3CDSENST00000452476ENST00000295550LYARchr4

4283622

+COL6A3chr2

238275370

+
intron-3CDSENST00000452476ENST00000472056LYARchr4

4283622

+COL6A3chr2

238275370

+
intron-3CDSENST00000452476ENST00000409809LYARchr4

4283622

+COL6A3chr2

238275370

+
intron-3CDSENST00000452476ENST00000346358LYARchr4

4283622

+COL6A3chr2

238275370

+
intron-intronENST00000452476ENST00000392004LYARchr4

4283622

+COL6A3chr2

238275370

+
intron-intronENST00000452476ENST00000392003LYARchr4

4283622

+COL6A3chr2

238275370

+
intron-intronENST00000452476ENST00000473258LYARchr4

4283622

+COL6A3chr2

238275370

+

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FusionProtFeatures for LYAR_COL6A3


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

Q9NX58

COL6A3

P12111

Plays a role in the maintenance of the appropriateprocessing of 47S/45S pre-rRNA to 32S/30S pre-rRNAs and theirsubsequent processing to produce 18S and 28S rRNAs(PubMed:24495227). Also acts at the level of transcriptionregulation. Along with PRMT5, binds the gamma-globin (HBG1/HBG2)promoter and represses its expression (PubMed:25092918). Inneuroblastoma cells, may also repress the expression of oxidativestress genes, including CHAC1, HMOX1, SLC7A11, ULBP1 and SNORD41that encodes a small nucleolar RNA (PubMed:28686580).Preferentially binds to a DNA motif containing 5'-GGTTAT-3'(PubMed:25092918). Stimulates phagocytosis of photoreceptor outersegments by retinal pigment epithelial cells (By similarity).Prevents nucleolin/NCL self-cleavage, maintaining a normal steady-state level of NCL protein in undifferentiated embryonic stemcells (ESCs), which in turn is essential for ESC self-renewal (Bysimilarity). {ECO:0000250|UniProtKB:Q08288,ECO:0000269|PubMed:24495227, ECO:0000269|PubMed:25092918,ECO:0000269|PubMed:28686580}.

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 LYAR_COL6A3


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 LYAR_COL6A3


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


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 LYAR_COL6A3


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 LYAR_COL6A3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneCOL6A3C1834674Bethlem myopathy4CTD_human;ORPHANET;UNIPROT
TgeneCOL6A3C0000786Spontaneous abortion1CTD_human
TgeneCOL6A3C0410179Scleroatonic muscular dystrophy1CTD_human;ORPHANET;UNIPROT
TgeneCOL6A3C4225336DYSTONIA 271ORPHANET;UNIPROT