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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:CYP39A1-LEMD2 (FusionGDB2 ID:HG51302TG221496)

Fusion Gene Summary for CYP39A1-LEMD2

check button Fusion gene summary
Fusion gene informationFusion gene name: CYP39A1-LEMD2
Fusion gene ID: hg51302tg221496
HgeneTgene
Gene symbol

CYP39A1

LEMD2

Gene ID

51302

221496

Gene namecytochrome P450 family 39 subfamily A member 1LEM domain nuclear envelope protein 2
Synonyms-CTRCT42|LEM2|NET25|dJ482C21.1
Cytomap('CYP39A1')('LEMD2')

6p12.3

6p21.31

Type of geneprotein-codingprotein-coding
Description24-hydroxycholesterol 7-alpha-hydroxylasecytochrome P450, family 39, subfamily A, polypeptide 1cytochrome P450, subfamily XXXIX (oxysterol 7 alpha-hydroxylase), polypeptide 1LEM domain-containing protein 2LEM domain containing 2hLEM2lamina-associated polypeptide-emerin-MAN1 domain containing 2
Modification date2020031320200313
UniProtAcc

Q9NYL5

Q8NC56

Ensembl transtripts involved in fusion geneENST00000275016, ENST00000489657, 
Fusion gene scores* DoF score3 X 3 X 3=276 X 6 X 2=72
# samples 36
** MAII scorelog2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(6/72*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CYP39A1 [Title/Abstract] AND LEMD2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCYP39A1(46620143)-LEMD2(33748930), # samples:3
Anticipated loss of major functional domain due to fusion event.CYP39A1-LEMD2 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
CYP39A1-LEMD2 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
* 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
HgeneCYP39A1

GO:0006699

bile acid biosynthetic process

10748047



check button Fusion gene information
* 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4KIRCTCGA-A3-3313-01ACYP39A1chr6

46620143

-LEMD2chr6

33748930

-


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Fusion Gene ORF analysis for CYP39A1-LEMD2

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
5CDS-5UTRENST00000275016ENST00000502643CYP39A1chr6

46620143

-LEMD2chr6

33748930

-
5CDS-5UTRENST00000275016ENST00000508327CYP39A1chr6

46620143

-LEMD2chr6

33748930

-
Frame-shiftENST00000275016ENST00000293760CYP39A1chr6

46620143

-LEMD2chr6

33748930

-
intron-3CDSENST00000489657ENST00000293760CYP39A1chr6

46620143

-LEMD2chr6

33748930

-
intron-5UTRENST00000489657ENST00000502643CYP39A1chr6

46620143

-LEMD2chr6

33748930

-
intron-5UTRENST00000489657ENST00000508327CYP39A1chr6

46620143

-LEMD2chr6

33748930

-

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for CYP39A1-LEMD2


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)


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Fusion Protein Features for CYP39A1-LEMD2


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:46620143/:33748930)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
CYP39A1

Q9NYL5

LEMD2

Q8NC56

FUNCTION: A cytochrome P450 monooxygenase involved in neural cholesterol clearance through bile acid synthesis (PubMed:25201972, PubMed:10748047). Catalyzes 7-alpha hydroxylation of (24S)-hydroxycholesterol, a neural oxysterol that is metabolized to bile acids in the liver (PubMed:25201972, PubMed:10748047). Mechanistically, uses molecular oxygen inserting one oxygen atom into a substrate, and reducing the second into a water molecule, with two electrons provided by NADPH via cytochrome P450 reductase (CPR; NADPH-ferrihemoprotein reductase) (PubMed:25201972, PubMed:10748047). {ECO:0000269|PubMed:10748047, ECO:0000269|PubMed:25201972}.FUNCTION: Involved in nuclear structure organization (PubMed:16339967). Required for maintaining the integrity of the nuclear envelope (PubMed:17097643). {ECO:0000269|PubMed:16339967, ECO:0000269|PubMed:17097643}.; FUNCTION: Required for embryonic development and is involved in regulation of several signaling pathways such as MAPK and AKT. Required for myoblast differentiation involving regulation of ERK signaling (By similarity). {ECO:0000250|UniProtKB:Q6DVA0}.

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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Fusion Gene Sequence for CYP39A1-LEMD2


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for CYP39A1-LEMD2


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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Related Drugs for CYP39A1-LEMD2


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for CYP39A1-LEMD2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCYP39A1C2239176Liver carcinoma1CTD_human
TgeneC0220721CATARACT 46, JUVENILE-ONSET1CTD_human;UNIPROT
TgeneC0266539Congenital total cataract1ORPHANET