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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: 35626

FusionGeneSummary for SPECC1L_SMARCB1

check button Fusion gene summary
Fusion gene informationFusion gene name: SPECC1L_SMARCB1
Fusion gene ID: 35626
HgeneTgene
Gene symbol

SPECC1L

SMARCB1

Gene ID

23384

6598

Gene namesperm antigen with calponin homology and coiled-coil domains 1 likeSWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1
SynonymsCYTSA|GBBB2|OBLFC1BAF47|CSS3|INI1|MRD15|PPP1R144|RDT|RTPS1|SNF5|SNF5L1|SWNTS1|Sfh1p|Snr1|hSNFS
Cytomap

22q11.23

22q11.23|22q11

Type of geneprotein-codingprotein-coding
Descriptioncytospin-ASPECC1-like proteincytokinesis and spindle organization Arenal carcinoma antigen NY-REN-22SWI/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 date2018052320180523
UniProtAcc

Q69YQ0

Q12824

Ensembl transtripts involved in fusion geneENST00000437398, ENST00000314328, 
ENST00000541492, ENST00000416735, 
ENST00000344921, ENST00000263121, 
ENST00000407422, ENST00000407082, 
ENST00000477836, 
Fusion gene scores* DoF score15 X 6 X 11=9903 X 7 X 3=63
# samples 1514
** MAII scorelog2(15/990*10)=-2.72246602447109
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(14/63*10)=1.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: SPECC1L [Title/Abstract] AND SMARCB1 [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
HgeneSPECC1L

GO:0007155

cell adhesion

21703590

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 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
TCGALDSTADTCGA-BR-8678-01ASPECC1Lchr22

24666951

+SMARCB1chr22

24133943

+
* 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-3CDSENST00000437398ENST00000344921SPECC1Lchr22

24666951

+SMARCB1chr22

24133943

+
5UTR-3CDSENST00000437398ENST00000263121SPECC1Lchr22

24666951

+SMARCB1chr22

24133943

+
5UTR-3CDSENST00000437398ENST00000407422SPECC1Lchr22

24666951

+SMARCB1chr22

24133943

+
5UTR-3CDSENST00000437398ENST00000407082SPECC1Lchr22

24666951

+SMARCB1chr22

24133943

+
5UTR-intronENST00000437398ENST00000477836SPECC1Lchr22

24666951

+SMARCB1chr22

24133943

+
5UTR-3CDSENST00000314328ENST00000344921SPECC1Lchr22

24666951

+SMARCB1chr22

24133943

+
5UTR-3CDSENST00000314328ENST00000263121SPECC1Lchr22

24666951

+SMARCB1chr22

24133943

+
5UTR-3CDSENST00000314328ENST00000407422SPECC1Lchr22

24666951

+SMARCB1chr22

24133943

+
5UTR-3CDSENST00000314328ENST00000407082SPECC1Lchr22

24666951

+SMARCB1chr22

24133943

+
5UTR-intronENST00000314328ENST00000477836SPECC1Lchr22

24666951

+SMARCB1chr22

24133943

+
5UTR-3CDSENST00000541492ENST00000344921SPECC1Lchr22

24666951

+SMARCB1chr22

24133943

+
5UTR-3CDSENST00000541492ENST00000263121SPECC1Lchr22

24666951

+SMARCB1chr22

24133943

+
5UTR-3CDSENST00000541492ENST00000407422SPECC1Lchr22

24666951

+SMARCB1chr22

24133943

+
5UTR-3CDSENST00000541492ENST00000407082SPECC1Lchr22

24666951

+SMARCB1chr22

24133943

+
5UTR-intronENST00000541492ENST00000477836SPECC1Lchr22

24666951

+SMARCB1chr22

24133943

+
3UTR-3CDSENST00000416735ENST00000344921SPECC1Lchr22

24666951

+SMARCB1chr22

24133943

+
3UTR-3CDSENST00000416735ENST00000263121SPECC1Lchr22

24666951

+SMARCB1chr22

24133943

+
3UTR-3CDSENST00000416735ENST00000407422SPECC1Lchr22

24666951

+SMARCB1chr22

24133943

+
3UTR-3CDSENST00000416735ENST00000407082SPECC1Lchr22

24666951

+SMARCB1chr22

24133943

+
3UTR-intronENST00000416735ENST00000477836SPECC1Lchr22

24666951

+SMARCB1chr22

24133943

+

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FusionProtFeatures for SPECC1L_SMARCB1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
SPECC1L

Q69YQ0

SMARCB1

Q12824

Involved in cytokinesis and spindle organization. Mayplay a role in actin cytoskeleton organization and microtubulestabilization and hence required for proper cell adhesion andmigration. {ECO:0000269|PubMed:21703590}. Core component of the BAF (hSWI/SNF) complex. This ATP-dependent chromatin-remodeling complex plays important roles incell proliferation and differentiation, in cellular antiviralactivities and inhibition of tumor formation. The BAF complex isable to create a stable, altered form of chromatin that constrainsfewer negative supercoils than normal. This change in supercoilingwould be due to the conversion of up to one-half of thenucleosomes on polynucleosomal arrays into asymmetric structures,termed altosomes, each composed of 2 histones octamers. Stimulatesin vitro the remodeling activity of SMARCA4/BRG1/BAF190A. Involvedin activation of CSF1 promoter. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and theneuron-specific chromatin remodeling complex (nBAF complex).During neural development a switch from a stem/progenitor to apostmitotic chromatin remodeling mechanism occurs as neurons exitthe cell cycle and become committed to their adult state. Thetransition from proliferating neural stem/progenitor cells topostmitotic neurons requires a switch in subunit composition ofthe npBAF and nBAF complexes. As neural progenitors exit mitosisand differentiate into neurons, npBAF complexes which containACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologousalternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunitsin neuron-specific complexes (nBAF). The npBAF complex isessential for the self-renewal/proliferative capacity of themultipotent neural stem cells. The nBAF complex along with CRESTplays a role regulating the activity of genes essential fordendrite growth (By similarity). Plays a key role in cell-cyclecontrol and causes cell cycle arrest in G0/G1.{ECO:0000250|UniProtKB:Q9Z0H3, ECO:0000269|PubMed:10078207,ECO:0000269|PubMed:12226744, ECO:0000269|PubMed:14604992,ECO:0000269|PubMed:16267391, ECO:0000269|PubMed:16314535,ECO:0000269|PubMed:9448295}.

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 SPECC1L_SMARCB1


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 SPECC1L_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
SPECC1LAPC, UBE2I, GLIS2, FBXO25, KIAA0368, UBC, PAN2, CCDC8, LUZP4, SLC25A41, ZNF219, KCTD17, FSD1, NFKBIA, LRFN4, RCN1, OBFC1, AP2M1, CHRNA9, SLC30A6, SPC25, HERC2, CAPZA2, CDK2, DBN1, MYH9, PPP1CB, IQGAP1, PDLIM7, SYNPO, ANLN, MYO5C, MYO19, MYO18A, C10orf2, LPXN, VAV1, ATMIN, ZNF785, G2E3, DUSP22, FEZ1, CCNJ, FSCN2, RPL15, G3BP1SMARCB1RELB, TACC2, SMARCA2, SMARCA4, SMARCC1, SIN3A, HDAC1, HDAC2, RBBP4, POLR2A, KLF1, GATA1, MYC, TP53, XPO1, RAN, YEATS4, MLLT10, BRCA1, SMARCB1, HSF1, SS18, ARID1A, ARID1B, SMARCC2, SMARCE1, ACTL6A, CCNE1, NCOR1, PPP1R15A, KMT2A, CREBBP, CDK8, MED21, KAT2B, PPP1CA, PPP1CB, PPP1CC, UBQLN4, ING1, MECP2, ING2, XPC, ATM, KMT2C, KMT2B, CDYL, MCPH1, BCL7C, AKT1, ACTA1, CDX2, PRMT5, SIN3B, TAF6, NR0B2, BCL2L11, SMARCD1, NONO, CARM1, EMD, DPF2, RB1CC1, RUNX1, PBRM1, ARID2, MAPK8IP2, GADD45G, CALR, TAF1D, RPS6KA5, PDPK1, MAP1LC3B, ZAK, SMARCAD1, SOX2, DPF3, CHFR, CEBPB, TFAP4, CUL3, COPS5, CAND1, APP, SMARCD2, SMARCD3, TOP2B, SAP18, EIF4A3, NCSTN, PHF10, VTN, TRA2A, SON, DPF1, EPAS1, ZDHHC17, BCL7A, BCL7B, CHMP4A, CPSF6, TBL1X, TBL1XR1, QSOX2, JUN, NFATC1, FOXN1, C1orf131, BARD1, BRCA2, ROR1, CDK9, APC, VHL, NR3C1, AR, DLST, ABI2, AES, ARL11, ATP5A1, DPH6, BHLHE40, BLZF1, FAM208B, CAMK2D, CCDC120, CCDC33, CCDC36, CD69, CDC23, CXCL11, CYB5D2, DNAJA3, FAM154A, FAM9B, GFAP, GOLGA2, HNRNPM, HOMEZ, HOOK2, HSFY1, IKZF3, KCTD9, KLC3, KPNA6, KRT15, KRT19, KRT6A, KRT6B, KRT6C, LDOC1, LENG8, LNX2, LY96, LZTS2, MBIP, MIF4GD, MXI1, NCK2, OSGIN1, OTX2, RINT1, RXRA, TEKT5, TFIP11, TNFAIP1, TNRC6A, TRIM27, TSC22D4, VIM, ZC3H11A, ZNF398


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 SPECC1L_SMARCB1


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 SPECC1L_SMARCB1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSPECC1LC1801950Opitz-G syndrome, type 21ORPHANET;UNIPROT
HgeneSPECC1LC1838348Oculomaxillofacial dysostosis1ORPHANET;UNIPROT
TgeneSMARCB1C0206743Rhabdoid Tumor2CTD_human
TgeneSMARCB1C3553248MENTAL RETARDATION, AUTOSOMAL DOMINANT 152UNIPROT
TgeneSMARCB1C0265338Coffin-Siris syndrome1CTD_human;ORPHANET
TgeneSMARCB1C1335929Schwannomatosis1CTD_human;ORPHANET