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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:MNAT1-SMARCB1 (FusionGDB2 ID:54143)

Fusion Gene Summary for MNAT1-SMARCB1

check button Fusion gene summary
Fusion gene informationFusion gene name: MNAT1-SMARCB1
Fusion gene ID: 54143
HgeneTgene
Gene symbol

MNAT1

SMARCB1

Gene ID

4331

6598

Gene nameMNAT1 component of CDK activating kinaseSWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1
SynonymsCAP35|MAT1|RNF66|TFB3BAF47|CSS3|INI1|MRD15|PPP1R144|RDT|RTPS1|SNF5|SNF5L1|SWNTS1|Sfh1p|Snr1|hSNFS
Cytomap

14q23.1

22q11.23|22q11

Type of geneprotein-codingprotein-coding
DescriptionCDK-activating kinase assembly factor MAT1CDK7/cyclin-H assembly factorMNAT CDK-activating kinase assembly factor 1MNAT1, CDK activating kinase assembly factorRING finger protein 66RING finger protein MAT1cyclin G1 interacting proteinmenage a troisSWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1BRG1-associated factor 47SNF5 homologSWI/SNF-related matrix-associated proteinhSNF5integrase interactor 1 proteinmalignant rhabdoid tumor suppressorprotein
Modification date2020031320200313
UniProtAcc

P51948

.
Ensembl transtripts involved in fusion geneENST00000555545, ENST00000261245, 
ENST00000539616, 		ENST00000344921, 
ENST00000263121, ENST00000407422, 
ENST00000407082, ENST00000477836, 
Fusion gene scores* DoF score10 X 6 X 7=42011 X 12 X 6=792
# samples 1017
** MAII scorelog2(10/420*10)=-2.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(17/792*10)=-2.21996568394191
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MNAT1 [Title/Abstract] AND SMARCB1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMNAT1(61305317)-SMARCB1(24175759), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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
HgeneMNAT1

GO:0006357

regulation of transcription by RNA polymerase II

10801852

HgeneMNAT1

GO:0006366

transcription by RNA polymerase II

9852112

HgeneMNAT1

GO:0045944

positive regulation of transcription by RNA polymerase II

8692841

HgeneMNAT1

GO:1905775

negative regulation of DNA helicase activity

11445587

TgeneSMARCB1

GO:0006337

nucleosome disassembly

8895581

TgeneSMARCB1

GO:0006338

chromatin remodeling

11726552

TgeneSMARCB1

GO:0039692

single stranded viral RNA replication via double stranded DNA intermediate

14963118

TgeneSMARCB1

GO:0045944

positive regulation of transcription by RNA polymerase II

11950834

TgeneSMARCB1

GO:0051091

positive regulation of DNA-binding transcription factor activity

11950834

TgeneSMARCB1

GO:1902661

positive regulation of glucose mediated signaling pathway

22368283


check buttonFusion gene breakpoints across MNAT1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across SMARCB1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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
ChimerDB4PRADTCGA-HC-8265MNAT1chr14

61305317

+SMARCB1chr22

24175759

+


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Fusion Gene ORF analysis for MNAT1-SMARCB1

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-3CDSENST00000555545ENST00000344921MNAT1chr14

61305317

+SMARCB1chr22

24175759

+
intron-3CDSENST00000555545ENST00000263121MNAT1chr14

61305317

+SMARCB1chr22

24175759

+
intron-3CDSENST00000555545ENST00000407422MNAT1chr14

61305317

+SMARCB1chr22

24175759

+
intron-3CDSENST00000555545ENST00000407082MNAT1chr14

61305317

+SMARCB1chr22

24175759

+
intron-intronENST00000555545ENST00000477836MNAT1chr14

61305317

+SMARCB1chr22

24175759

+
intron-3CDSENST00000261245ENST00000344921MNAT1chr14

61305317

+SMARCB1chr22

24175759

+
intron-3CDSENST00000261245ENST00000263121MNAT1chr14

61305317

+SMARCB1chr22

24175759

+
intron-3CDSENST00000261245ENST00000407422MNAT1chr14

61305317

+SMARCB1chr22

24175759

+
intron-3CDSENST00000261245ENST00000407082MNAT1chr14

61305317

+SMARCB1chr22

24175759

+
intron-intronENST00000261245ENST00000477836MNAT1chr14

61305317

+SMARCB1chr22

24175759

+
intron-3CDSENST00000539616ENST00000344921MNAT1chr14

61305317

+SMARCB1chr22

24175759

+
intron-3CDSENST00000539616ENST00000263121MNAT1chr14

61305317

+SMARCB1chr22

24175759

+
intron-3CDSENST00000539616ENST00000407422MNAT1chr14

61305317

+SMARCB1chr22

24175759

+
intron-3CDSENST00000539616ENST00000407082MNAT1chr14

61305317

+SMARCB1chr22

24175759

+
intron-intronENST00000539616ENST00000477836MNAT1chr14

61305317

+SMARCB1chr22

24175759

+

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 MNAT1-SMARCB1


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. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

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.

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Fusion Protein Features for MNAT1-SMARCB1


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
MNAT1

P51948

.
FUNCTION: Stabilizes the cyclin H-CDK7 complex to form a functional CDK-activating kinase (CAK) enzymatic complex. CAK activates the cyclin-associated kinases CDK1, CDK2, CDK4 and CDK6 by threonine phosphorylation. CAK complexed to the core-TFIIH basal transcription factor activates RNA polymerase II by serine phosphorylation of the repetitive C-terminal domain (CTD) of its large subunit (POLR2A), allowing its escape from the promoter and elongation of the transcripts. Involved in cell cycle control and in RNA transcription by RNA polymerase II. {ECO:0000269|PubMed:10024882}.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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 MNAT1-SMARCB1


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 MNAT1-SMARCB1


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 MNAT1-SMARCB1


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 MNAT1-SMARCB1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneSMARCB1C0206743Rhabdoid Tumor10CGI;CLINGEN;CTD_human
TgeneSMARCB1C1836327RHABDOID TUMOR PREDISPOSITION SYNDROME 1 (disorder)10CLINGEN;CTD_human;GENOMICS_ENGLAND
TgeneSMARCB1C1266184Atypical Teratoid Rhabdoid Tumor8CLINGEN;ORPHANET
TgeneSMARCB1C1836326Teratoid Tumor, Atypical8CLINGEN
TgeneSMARCB1C2750405Malignant Rhabdoid Tumor, Somatic8CLINGEN;CTD_human
TgeneSMARCB1C1335929Schwannomatosis4CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneSMARCB1C3553248MENTAL RETARDATION, AUTOSOMAL DOMINANT 153GENOMICS_ENGLAND;UNIPROT
TgeneSMARCB1C0917817Neurofibromatosis 32ORPHANET
TgeneSMARCB1C2931480Neurofibromatosis, Type 3, mixed central and peripheral2ORPHANET
TgeneSMARCB1C0025286Meningioma1ORPHANET
TgeneSMARCB1C0265338Coffin-Siris syndrome1CTD_human;GENOMICS_ENGLAND
TgeneSMARCB1C2985524Rhabdoid tumor predisposition syndrome1ORPHANET
TgeneSMARCB1C4048809SCHWANNOMATOSIS 11CTD_human