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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: 34799

FusionGeneSummary for SMARCA4_PTMA

check button Fusion gene summary
Fusion gene informationFusion gene name: SMARCA4_PTMA
Fusion gene ID: 34799
HgeneTgene
Gene symbol

SMARCA4

PTMA

Gene ID

6597

5757

Gene nameSWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4prothymosin alpha
SynonymsBAF190|BAF190A|BRG1|CSS4|MRD16|RTPS2|SNF2|SNF2L4|SNF2LB|SWI2|hSNF2bTMSA
Cytomap

19p13.2

2q37.1

Type of geneprotein-codingprotein-coding
Descriptiontranscription activator BRG1ATP-dependent helicase SMARCA4BRG1-associated factor 190ABRM/SWI2-related gene 1SNF2-betaSNF2-like 4brahma protein-like 1global transcription activator homologous sequencehomeotic gene regulatormitotic growth and transprothymosin alphagene sequence 28prothymosin alpha proteinprothymosin-I+/-
Modification date2018052320180522
UniProtAcc

P51532

P06454

Ensembl transtripts involved in fusion geneENST00000358026, ENST00000344626, 
ENST00000429416, ENST00000541122, 
ENST00000589677, ENST00000444061, 
ENST00000590574, ENST00000413806, 
ENST00000450717, ENST00000538456, 
ENST00000466801, ENST00000409321, 
ENST00000409115, ENST00000341369, 
ENST00000409683, ENST00000410064, 
Fusion gene scores* DoF score20 X 20 X 15=600017 X 17 X 2=578
# samples 3218
** MAII scorelog2(32/6000*10)=-4.22881869049588
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(18/578*10)=-1.683072586171
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SMARCA4 [Title/Abstract] AND PTMA [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
HgeneSMARCA4

GO:0006337

nucleosome disassembly

8895581

HgeneSMARCA4

GO:0006338

chromatin remodeling

10943845|11726552

HgeneSMARCA4

GO:0045892

negative regulation of transcription, DNA-templated

12065415

HgeneSMARCA4

GO:0045944

positive regulation of transcription by RNA polymerase II

15774904|17938176

HgeneSMARCA4

GO:0051091

positive regulation of DNA binding transcription factor activity

11950834|17938176

HgeneSMARCA4

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
ChiTaRS3.1CN347182SMARCA4chr19

11145730

+PTMAchr2

232576658

+
* 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
5CDS-3UTRENST00000358026ENST00000466801SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000358026ENST00000409321SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000358026ENST00000409115SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000358026ENST00000341369SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000358026ENST00000409683SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000358026ENST00000410064SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000344626ENST00000466801SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000344626ENST00000409321SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000344626ENST00000409115SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000344626ENST00000341369SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000344626ENST00000409683SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000344626ENST00000410064SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000429416ENST00000466801SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000429416ENST00000409321SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000429416ENST00000409115SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000429416ENST00000341369SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000429416ENST00000409683SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000429416ENST00000410064SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000541122ENST00000466801SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000541122ENST00000409321SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000541122ENST00000409115SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000541122ENST00000341369SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000541122ENST00000409683SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000541122ENST00000410064SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000589677ENST00000466801SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000589677ENST00000409321SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000589677ENST00000409115SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000589677ENST00000341369SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000589677ENST00000409683SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000589677ENST00000410064SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000444061ENST00000466801SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000444061ENST00000409321SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000444061ENST00000409115SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000444061ENST00000341369SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000444061ENST00000409683SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000444061ENST00000410064SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000590574ENST00000466801SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000590574ENST00000409321SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000590574ENST00000409115SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000590574ENST00000341369SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000590574ENST00000409683SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000590574ENST00000410064SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000413806ENST00000466801SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000413806ENST00000409321SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000413806ENST00000409115SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000413806ENST00000341369SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000413806ENST00000409683SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000413806ENST00000410064SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000450717ENST00000466801SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000450717ENST00000409321SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000450717ENST00000409115SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000450717ENST00000341369SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000450717ENST00000409683SMARCA4chr19

11145730

+PTMAchr2

232576658

+
5CDS-3UTRENST00000450717ENST00000410064SMARCA4chr19

11145730

+PTMAchr2

232576658

+
3UTR-3UTRENST00000538456ENST00000466801SMARCA4chr19

11145730

+PTMAchr2

232576658

+
3UTR-3UTRENST00000538456ENST00000409321SMARCA4chr19

11145730

+PTMAchr2

232576658

+
3UTR-3UTRENST00000538456ENST00000409115SMARCA4chr19

11145730

+PTMAchr2

232576658

+
3UTR-3UTRENST00000538456ENST00000341369SMARCA4chr19

11145730

+PTMAchr2

232576658

+
3UTR-3UTRENST00000538456ENST00000409683SMARCA4chr19

11145730

+PTMAchr2

232576658

+
3UTR-3UTRENST00000538456ENST00000410064SMARCA4chr19

11145730

+PTMAchr2

232576658

+

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FusionProtFeatures for SMARCA4_PTMA


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
SMARCA4

P51532

PTMA

P06454

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. Component of the CREST-BRG1 complex, amultiprotein complex that regulates promoter activation byorchestrating the calcium-dependent release of a repressor complexand the recruitment of an activator complex. In resting neurons,transcription of the c-FOS promoter is inhibited by SMARCA4-dependent recruitment of a phospho-RB1-HDAC repressor complex.Upon calcium influx, RB1 is dephosphorylated by calcineurin, whichleads to release of the repressor complex. At the same time, thereis 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, andactivity-dependent induction of NR2B expression involves therelease of HDAC1 and recruitment of CREBBP. Belongs to the neuralprogenitors-specific chromatin remodeling complex (npBAF complex)and the neuron-specific chromatin remodeling complex (nBAFcomplex). 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. SMARCA4/BAF190A may promote neuralstem cell self-renewal/proliferation by enhancing Notch-dependentproliferative signals, while concurrently making the neural stemcell insensitive to SHH-dependent differentiating cues (Bysimilarity). Acts as a corepressor of ZEB1 to regulate E-cadherintranscription and is required for induction of epithelial-mesenchymal transition (EMT) by ZEB1. Binds via DLX1 to enhancerslocated in the intergenic region between DLX5 and DLX6 and thisbinding is stabilized by the long non-coding RNA (lncRNA) Evf2 (Bysimilarity). Binds to RNA in a promiscuous manner (By similarity).Binding to RNAs including lncRNA Evf2 leads to inhibition ofSMARCA4 ATPase and chromatin remodeling activities (Bysimilarity). {ECO:0000250|UniProtKB:Q3TKT4,ECO:0000269|PubMed:19571879, ECO:0000269|PubMed:20418909,ECO:0000303|PubMed:22952240, ECO:0000303|PubMed:26601204}. Prothymosin alpha may mediate immune function byconferring resistance to certain opportunistic infections.

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 SMARCA4_PTMA


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 SMARCA4_PTMA


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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RelatedDrugs for SMARCA4_PTMA


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 SMARCA4_PTMA


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSMARCA4C0262584Carcinoma, Small Cell4CTD_human
HgeneSMARCA4C0919267ovarian neoplasm4CTD_human
HgeneSMARCA4C0006413Burkitt Lymphoma1CTD_human
HgeneSMARCA4C0036920Sezary Syndrome1CTD_human
HgeneSMARCA4C0039981Thoracic Neoplasms1CTD_human
HgeneSMARCA4C0149925Small cell carcinoma of lung1CTD_human
HgeneSMARCA4C0265338Coffin-Siris syndrome1CTD_human;ORPHANET
HgeneSMARCA4C1261473Sarcoma1CTD_human
HgeneSMARCA4C3553249MENTAL RETARDATION, AUTOSOMAL DOMINANT 161UNIPROT
TgenePTMAC0001430Adenoma1CTD_human
TgenePTMAC0015695Fatty Liver1CTD_human
TgenePTMAC0024121Lung Neoplasms1CTD_human
TgenePTMAC0035412Rhabdomyosarcoma1CTD_human