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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: 32779

FusionGeneSummary for SCAP_SMARCC1

check button Fusion gene summary
Fusion gene informationFusion gene name: SCAP_SMARCC1
Fusion gene ID: 32779
HgeneTgene
Gene symbol

SCAP

SMARCC1

Gene ID

22937

6599

Gene nameSREBF chaperoneSWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 1
Synonyms-BAF155|CRACC1|Rsc8|SRG3|SWI3
Cytomap

3p21.31

3p21.31

Type of geneprotein-codingprotein-coding
Descriptionsterol regulatory element-binding protein cleavage-activating proteinSREBP cleavage-activating proteinSWI/SNF complex subunit SMARCC1BRG1-associated factor 155SWI/SNF complex 155 kDa subunitSWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C member 1chromatin remodeling complex BAF155 subunitmammalian chromatin remode
Modification date2018052220180523
UniProtAcc

Q12770

Q92922

Ensembl transtripts involved in fusion geneENST00000265565, ENST00000441517, 
ENST00000545718, ENST00000465628, 
ENST00000254480, ENST00000425518, 
Fusion gene scores* DoF score4 X 2 X 3=2412 X 12 X 4=576
# samples 413
** MAII scorelog2(4/24*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(13/576*10)=-2.14755718841386
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SCAP [Title/Abstract] AND SMARCC1 [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
TgeneSMARCC1

GO:0006337

nucleosome disassembly

8895581

TgeneSMARCC1

GO:0006338

chromatin remodeling

10078207|11018012|11726552

TgeneSMARCC1

GO:0045893

positive regulation of transcription, DNA-templated

11018012


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
TCGARVHNSCTCGA-CV-6962-01ASCAPchr3

47517289

-SMARCC1chr3

47712207

-
* 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
5UTR-3CDSENST00000265565ENST00000254480SCAPchr3

47517289

-SMARCC1chr3

47712207

-
5UTR-5UTRENST00000265565ENST00000425518SCAPchr3

47517289

-SMARCC1chr3

47712207

-
5UTR-3CDSENST00000441517ENST00000254480SCAPchr3

47517289

-SMARCC1chr3

47712207

-
5UTR-5UTRENST00000441517ENST00000425518SCAPchr3

47517289

-SMARCC1chr3

47712207

-
5UTR-3CDSENST00000545718ENST00000254480SCAPchr3

47517289

-SMARCC1chr3

47712207

-
5UTR-5UTRENST00000545718ENST00000425518SCAPchr3

47517289

-SMARCC1chr3

47712207

-
intron-3CDSENST00000465628ENST00000254480SCAPchr3

47517289

-SMARCC1chr3

47712207

-
intron-5UTRENST00000465628ENST00000425518SCAPchr3

47517289

-SMARCC1chr3

47712207

-

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FusionProtFeatures for SCAP_SMARCC1


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

Q12770

SMARCC1

Q92922

Escort protein required for cholesterol as well as lipidhomeostasis. Regulates export of the SCAP/SREBF complex from theER upon low cholesterol. Formation of a ternary complex with INSIGat high sterol concentrations leads to masking of an ER-exportsignal in SCAP and retention of the complex in the ER. Low sterolconcentrations trigger release of INSIG, a conformational changein the SSC domain of SCAP, unmasking of the ER export signal,recruitment into COPII-coated vesicles, transport to the Golgicomplex, proteolytic cleavage of SREBF in the Golgi, release ofthe transcription factor fragment of SREBF from the membrane, itsimport into the nucleus and up-regulation of LDLR, INSIG1 and themevalonate pathway (By similarity). {ECO:0000250}. Involved in transcriptional activation and repression ofselect genes by chromatin remodeling (alteration of DNA-nucleosometopology). Component of SWI/SNF chromatin remodeling complexesthat carry out key enzymatic activities, changing chromatinstructure by altering DNA-histone contacts within a nucleosome inan ATP-dependent manner. May stimulate the ATPase activity of thecatalytic subunit of the complex (PubMed:10078207). Belongs to theneural progenitors-specific chromatin remodeling complex (npBAFcomplex) and the neuron-specific chromatin remodeling complex(nBAF complex). During neural development a switch from astem/progenitor to a postmitotic chromatin remodeling mechanismoccurs as neurons exit the cell cycle and become committed totheir adult state. The transition from proliferating neuralstem/progenitor cells to postmitotic neurons requires a switch insubunit composition of the npBAF and nBAF complexes. As neuralprogenitors exit mitosis and differentiate into neurons, npBAFcomplexes which contain ACTL6A/BAF53A and PHF10/BAF45A, areexchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45Bor DPF3/BAF45C subunits in neuron-specific complexes (nBAF). ThenpBAF complex is essential for the self-renewal/proliferativecapacity of the multipotent neural stem cells. The nBAF complexalong with CREST plays a role regulating the activity of genesessential for dendrite growth (By similarity).{ECO:0000250|UniProtKB:P97496, ECO:0000269|PubMed:10078207,ECO:0000269|PubMed:11018012, ECO:0000303|PubMed:22952240,ECO:0000303|PubMed:26601204}.

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 SCAP_SMARCC1


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 SCAP_SMARCC1


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
SCAPINSIG1, INSIG2, RNF139, SEC24B, SREBF1, SREBF2, ERLIN2, MOV10, NXF1, MCOLN3, NAALADL2, HLA-C, ATP1B4, BTNL8, LPAR1, GLRA2, RPTOR, IPPK, ZNRF4, B4GAT1SMARCC1RELB, NR3C1, SMARCD1, SMARCB1, SMARCA4, SMARCA2, SIN3A, KLF1, GATA1, SP1, TP53, BRCA1, STAT2, CCNE1, HSP90B1, NCOR1, SMARCE1, CEBPB, CDK8, ING1, AR, ING2, TAF10, NR4A1, ARID1A, SMARCC2, PBRM1, ADD1, MCPH1, BCL7C, BRD7, ARID1B, AKT1, PRMT5, MYC, SMARCC1, HNRNPC, CHD4, SRRM2, TAF6, NR0B2, NONO, SMAD2, SMAD3, CARM1, EMD, DPF2, TRIM28, RUNX1, CHD7, ARID2, STK11, WHSC1L1, SMARCAD1, SOX2, ELAVL1, SIRT7, DPF3, PHF10, DPF1, ACTL6A, CUL3, CAND1, BAZ1B, SMARCD2, TOP2B, HDAC1, SMARCA5, RBBP5, KDM1A, SMARCA1, NOTCH1, EPAS1, VCP, HDAC6, ITCH, NEDD4, WWOX, AURKB, OTX1, PLSCR1, ADAMTSL4, MOV10, NXF1, MSL1, EED, RNF2, BMI1, SS18, NTRK1, MESDC2, MRE11A, SAMD9, BCL7A, CPSF6, DCTN2, FUBP1, FUBP3, KHSRP, MDC1, METTL13, NCAPH2, SF3A1, TMOD3, YLPM1, SMARCD3, SS18L1, TBL1XR1, NCOA1, KMT2A, EWSR1, HIST1H3E, RAB5C, NR2C2, FOS, JUN, NFATC1, NFATC2, C1orf131, SFPQ, CHEK1, TRIM25


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 SCAP_SMARCC1


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 SCAP_SMARCC1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSCAPC2239176Liver carcinoma1CTD_human
TgeneSMARCC1C0001418Adenocarcinoma1CTD_human
TgeneSMARCC1C0023893Liver Cirrhosis, Experimental1CTD_human
TgeneSMARCC1C0024121Lung Neoplasms1CTD_human