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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:SMARCA2-NFIB (FusionGDB2 ID:83292)

Fusion Gene Summary for SMARCA2-NFIB

check button Fusion gene summary
Fusion gene informationFusion gene name: SMARCA2-NFIB
Fusion gene ID: 83292
HgeneTgene
Gene symbol

SMARCA2

NFIB

Gene ID

6595

4781

Gene nameSWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2nuclear factor I B
SynonymsBAF190|BRM|NCBRS|SNF2|SNF2L2|SNF2LA|SWI2|Sth1p|hBRM|hSNF2aCTF|HMGIC/NFIB|MACID|NF-I/B|NF1-B|NFI-B|NFI-RED|NFIB2|NFIB3
Cytomap

9p24.3

9p23-p22.3

Type of geneprotein-codingprotein-coding
Descriptionprobable global transcription activator SNF2L2ATP-dependent helicase SMARCA2BAF190BBRG1-associated factor 190BSNF2-alphaSNF2/SWI2-like protein 2SWI/SNF-related matrix-associated actin-dependent regulator of chromatin a2brahma homologglobal transcrnuclear factor 1 B-typeCCAAT-box-binding transcription factorTGGCA-binding proteinnuclear factor 1/B
Modification date2020031520200313
UniProtAcc.

O00712

Ensembl transtripts involved in fusion geneENST00000357248, ENST00000349721, 
ENST00000382203, ENST00000382194, 
ENST00000491574, ENST00000324954, 
ENST00000302401, ENST00000382186, 
ENST00000382185, 		ENST00000380934, 
ENST00000380959, ENST00000380953, 
ENST00000397575, ENST00000397581, 
ENST00000397579, ENST00000543693, 
ENST00000380924, ENST00000380921, 
Fusion gene scores* DoF score14 X 9 X 10=126013 X 23 X 8=2392
# samples 1517
** MAII scorelog2(15/1260*10)=-3.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(17/2392*10)=-3.8146107380604
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SMARCA2 [Title/Abstract] AND NFIB [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSMARCA2(2015404)-NFIB(14179779), # 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
HgeneSMARCA2

GO:0008285

negative regulation of cell proliferation

14660596

HgeneSMARCA2

GO:0045892

negative regulation of transcription, DNA-templated

12065415

HgeneSMARCA2

GO:0045893

positive regulation of transcription, DNA-templated

17984088

HgeneSMARCA2

GO:0045944

positive regulation of transcription by RNA polymerase II

15774904

TgeneNFIB

GO:0045893

positive regulation of transcription, DNA-templated

30388402

TgeneNFIB

GO:0045944

positive regulation of transcription by RNA polymerase II

9099724|19540848


check buttonFusion gene breakpoints across SMARCA2 (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 NFIB (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
ChimerDB4STADTCGA-HU-A4GN-01ASMARCA2chr9

2015404

+NFIBchr9

14179779

-


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Fusion Gene ORF analysis for SMARCA2-NFIB

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
5UTR-3CDSENST00000357248ENST00000380934SMARCA2chr9

2015404

+NFIBchr9

14179779

-
5UTR-3CDSENST00000357248ENST00000380959SMARCA2chr9

2015404

+NFIBchr9

14179779

-
5UTR-3CDSENST00000357248ENST00000380953SMARCA2chr9

2015404

+NFIBchr9

14179779

-
5UTR-3CDSENST00000357248ENST00000397575SMARCA2chr9

2015404

+NFIBchr9

14179779

-
5UTR-3CDSENST00000357248ENST00000397581SMARCA2chr9

2015404

+NFIBchr9

14179779

-
5UTR-3CDSENST00000357248ENST00000397579SMARCA2chr9

2015404

+NFIBchr9

14179779

-
5UTR-5UTRENST00000357248ENST00000543693SMARCA2chr9

2015404

+NFIBchr9

14179779

-
5UTR-5UTRENST00000357248ENST00000380924SMARCA2chr9

2015404

+NFIBchr9

14179779

-
5UTR-intronENST00000357248ENST00000380921SMARCA2chr9

2015404

+NFIBchr9

14179779

-
5UTR-3CDSENST00000349721ENST00000380934SMARCA2chr9

2015404

+NFIBchr9

14179779

-
5UTR-3CDSENST00000349721ENST00000380959SMARCA2chr9

2015404

+NFIBchr9

14179779

-
5UTR-3CDSENST00000349721ENST00000380953SMARCA2chr9

2015404

+NFIBchr9

14179779

-
5UTR-3CDSENST00000349721ENST00000397575SMARCA2chr9

2015404

+NFIBchr9

14179779

-
5UTR-3CDSENST00000349721ENST00000397581SMARCA2chr9

2015404

+NFIBchr9

14179779

-
5UTR-3CDSENST00000349721ENST00000397579SMARCA2chr9

2015404

+NFIBchr9

14179779

-
5UTR-5UTRENST00000349721ENST00000543693SMARCA2chr9

2015404

+NFIBchr9

14179779

-
5UTR-5UTRENST00000349721ENST00000380924SMARCA2chr9

2015404

+NFIBchr9

14179779

-
5UTR-intronENST00000349721ENST00000380921SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000382203ENST00000380934SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000382203ENST00000380959SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000382203ENST00000380953SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000382203ENST00000397575SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000382203ENST00000397581SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000382203ENST00000397579SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-5UTRENST00000382203ENST00000543693SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-5UTRENST00000382203ENST00000380924SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-intronENST00000382203ENST00000380921SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000382194ENST00000380934SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000382194ENST00000380959SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000382194ENST00000380953SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000382194ENST00000397575SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000382194ENST00000397581SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000382194ENST00000397579SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-5UTRENST00000382194ENST00000543693SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-5UTRENST00000382194ENST00000380924SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-intronENST00000382194ENST00000380921SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000491574ENST00000380934SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000491574ENST00000380959SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000491574ENST00000380953SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000491574ENST00000397575SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000491574ENST00000397581SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000491574ENST00000397579SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-5UTRENST00000491574ENST00000543693SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-5UTRENST00000491574ENST00000380924SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-intronENST00000491574ENST00000380921SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000324954ENST00000380934SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000324954ENST00000380959SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000324954ENST00000380953SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000324954ENST00000397575SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000324954ENST00000397581SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000324954ENST00000397579SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-5UTRENST00000324954ENST00000543693SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-5UTRENST00000324954ENST00000380924SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-intronENST00000324954ENST00000380921SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000302401ENST00000380934SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000302401ENST00000380959SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000302401ENST00000380953SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000302401ENST00000397575SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000302401ENST00000397581SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000302401ENST00000397579SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-5UTRENST00000302401ENST00000543693SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-5UTRENST00000302401ENST00000380924SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-intronENST00000302401ENST00000380921SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000382186ENST00000380934SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000382186ENST00000380959SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000382186ENST00000380953SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000382186ENST00000397575SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000382186ENST00000397581SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000382186ENST00000397579SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-5UTRENST00000382186ENST00000543693SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-5UTRENST00000382186ENST00000380924SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-intronENST00000382186ENST00000380921SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000382185ENST00000380934SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000382185ENST00000380959SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000382185ENST00000380953SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000382185ENST00000397575SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000382185ENST00000397581SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-3CDSENST00000382185ENST00000397579SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-5UTRENST00000382185ENST00000543693SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-5UTRENST00000382185ENST00000380924SMARCA2chr9

2015404

+NFIBchr9

14179779

-
intron-intronENST00000382185ENST00000380921SMARCA2chr9

2015404

+NFIBchr9

14179779

-

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 SMARCA2-NFIB


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 SMARCA2-NFIB


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
.NFIB

O00712

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.FUNCTION: Transcriptional activator of GFAP, essential for proper brain development (PubMed:30388402). Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication. {ECO:0000269|PubMed:30388402}.

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 SMARCA2-NFIB


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 SMARCA2-NFIB


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 SMARCA2-NFIB


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 SMARCA2-NFIB


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSMARCA2C0036341Schizophrenia4PSYGENET
HgeneSMARCA2C1303073Nicolaides Baraitser syndrome4CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneSMARCA2C0010606Adenoid Cystic Carcinoma1CTD_human
HgeneSMARCA2C0265338Coffin-Siris syndrome1CTD_human;GENOMICS_ENGLAND
HgeneSMARCA2C0345967Malignant mesothelioma1CTD_human
HgeneSMARCA2C3281201MENTAL RETARDATION, AUTOSOMAL DOMINANT 121GENOMICS_ENGLAND
TgeneNFIBC0010606Adenoid Cystic Carcinoma1CTD_human
TgeneNFIBC0221355Macrocephaly1GENOMICS_ENGLAND
TgeneNFIBC0557874Global developmental delay1GENOMICS_ENGLAND
TgeneNFIBC3714756Intellectual Disability1GENOMICS_ENGLAND
TgeneNFIBC4748993MACROCEPHALY, ACQUIRED, WITH IMPAIRED INTELLECTUAL DEVELOPMENT1GENOMICS_ENGLAND;UNIPROT