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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:MKRN1-NLGN1 (FusionGDB2 ID:HG23608TG22871)

Fusion Gene Summary for MKRN1-NLGN1

check button Fusion gene summary
Fusion gene informationFusion gene name: MKRN1-NLGN1
Fusion gene ID: hg23608tg22871
HgeneTgene
Gene symbol

MKRN1

NLGN1

Gene ID

23608

22871

Gene namemakorin ring finger protein 1neuroligin 1
SynonymsRNF61NL1
Cytomap('MKRN1')('NLGN1')

7q34

3q26.31

Type of geneprotein-codingprotein-coding
DescriptionE3 ubiquitin-protein ligase makorin-1RING finger protein 61RING-type E3 ubiquitin transferase makorin-1neuroligin-1
Modification date2020031320200313
UniProtAcc

Q9UHC7

.
Ensembl transtripts involved in fusion geneENST00000255977, ENST00000443720, 
ENST00000474576, ENST00000480552, 
ENST00000437223, ENST00000481705, 
Fusion gene scores* DoF score10 X 11 X 9=99013 X 8 X 9=936
# samples 1515
** MAII scorelog2(15/990*10)=-2.72246602447109
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(15/936*10)=-2.64154602908752
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MKRN1 [Title/Abstract] AND NLGN1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMKRN1(140171683)-NLGN1(173993105), # samples:2
Anticipated loss of major functional domain due to fusion event.MKRN1-NLGN1 seems lost the major protein functional domain in Hgene 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
HgeneMKRN1

GO:0000209

protein polyubiquitination

19536131

TgeneNLGN1

GO:0031175

neuron projection development

22750515

TgeneNLGN1

GO:0051965

positive regulation of synapse assembly

24613359



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
ChimerDB4SARCTCGA-DX-A23R-01AMKRN1chr7

140171683

-NLGN1chr3

173993105

+


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Fusion Gene ORF analysis for MKRN1-NLGN1

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-3UTRENST00000255977ENST00000466350MKRN1chr7

140171683

-NLGN1chr3

173993105

+
5CDS-3UTRENST00000443720ENST00000466350MKRN1chr7

140171683

-NLGN1chr3

173993105

+
5CDS-3UTRENST00000474576ENST00000466350MKRN1chr7

140171683

-NLGN1chr3

173993105

+
5CDS-3UTRENST00000480552ENST00000466350MKRN1chr7

140171683

-NLGN1chr3

173993105

+
5UTR-3CDSENST00000437223ENST00000361589MKRN1chr7

140171683

-NLGN1chr3

173993105

+
5UTR-3CDSENST00000437223ENST00000401917MKRN1chr7

140171683

-NLGN1chr3

173993105

+
5UTR-3CDSENST00000437223ENST00000457714MKRN1chr7

140171683

-NLGN1chr3

173993105

+
5UTR-3CDSENST00000437223ENST00000545397MKRN1chr7

140171683

-NLGN1chr3

173993105

+
5UTR-3CDSENST00000481705ENST00000361589MKRN1chr7

140171683

-NLGN1chr3

173993105

+
5UTR-3CDSENST00000481705ENST00000401917MKRN1chr7

140171683

-NLGN1chr3

173993105

+
5UTR-3CDSENST00000481705ENST00000457714MKRN1chr7

140171683

-NLGN1chr3

173993105

+
5UTR-3CDSENST00000481705ENST00000545397MKRN1chr7

140171683

-NLGN1chr3

173993105

+
5UTR-3UTRENST00000437223ENST00000466350MKRN1chr7

140171683

-NLGN1chr3

173993105

+
5UTR-3UTRENST00000481705ENST00000466350MKRN1chr7

140171683

-NLGN1chr3

173993105

+
Frame-shiftENST00000255977ENST00000361589MKRN1chr7

140171683

-NLGN1chr3

173993105

+
Frame-shiftENST00000255977ENST00000401917MKRN1chr7

140171683

-NLGN1chr3

173993105

+
Frame-shiftENST00000255977ENST00000457714MKRN1chr7

140171683

-NLGN1chr3

173993105

+
Frame-shiftENST00000255977ENST00000545397MKRN1chr7

140171683

-NLGN1chr3

173993105

+
Frame-shiftENST00000443720ENST00000361589MKRN1chr7

140171683

-NLGN1chr3

173993105

+
Frame-shiftENST00000443720ENST00000401917MKRN1chr7

140171683

-NLGN1chr3

173993105

+
Frame-shiftENST00000443720ENST00000457714MKRN1chr7

140171683

-NLGN1chr3

173993105

+
Frame-shiftENST00000443720ENST00000545397MKRN1chr7

140171683

-NLGN1chr3

173993105

+
Frame-shiftENST00000474576ENST00000361589MKRN1chr7

140171683

-NLGN1chr3

173993105

+
Frame-shiftENST00000474576ENST00000401917MKRN1chr7

140171683

-NLGN1chr3

173993105

+
Frame-shiftENST00000474576ENST00000457714MKRN1chr7

140171683

-NLGN1chr3

173993105

+
Frame-shiftENST00000474576ENST00000545397MKRN1chr7

140171683

-NLGN1chr3

173993105

+
Frame-shiftENST00000480552ENST00000361589MKRN1chr7

140171683

-NLGN1chr3

173993105

+
Frame-shiftENST00000480552ENST00000401917MKRN1chr7

140171683

-NLGN1chr3

173993105

+
Frame-shiftENST00000480552ENST00000457714MKRN1chr7

140171683

-NLGN1chr3

173993105

+
Frame-shiftENST00000480552ENST00000545397MKRN1chr7

140171683

-NLGN1chr3

173993105

+

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 MKRN1-NLGN1


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)


check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.
genomic feature of top 1%

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Fusion Protein Features for MKRN1-NLGN1


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/:140171683/:173993105)
- 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
MKRN1

Q9UHC7

.
FUNCTION: E3 ubiquitin ligase catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins. These substrates include FILIP1, p53/TP53, CDKN1A and TERT. Keeps cells alive by suppressing p53/TP53 under normal conditions, but stimulates apoptosis by repressing CDKN1A under stress conditions. Acts as a negative regulator of telomerase. Has negative and positive effects on RNA polymerase II-dependent transcription. {ECO:0000269|PubMed:16785614, ECO:0000269|PubMed:19536131}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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 MKRN1-NLGN1


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 MKRN1-NLGN1


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 MKRN1-NLGN1


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 MKRN1-NLGN1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0004352Autistic Disorder1CTD_human
TgeneC0005586Bipolar Disorder1PSYGENET
TgeneC0036341Schizophrenia1PSYGENET
TgeneC3495676Anorectal Malformations1GENOMICS_ENGLAND