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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: 34838

FusionGeneSummary for SMARCD1_ATP2C2

check button Fusion gene summary
Fusion gene informationFusion gene name: SMARCD1_ATP2C2
Fusion gene ID: 34838
HgeneTgene
Gene symbol

SMARCD1

ATP2C2

Gene ID

6602

9914

Gene nameSWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1ATPase secretory pathway Ca2+ transporting 2
SynonymsBAF60A|CRACD1|Rsc6pSPCA2
Cytomap

12q13.12

16q24.1

Type of geneprotein-codingprotein-coding
DescriptionSWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 160 kDa BRG-1/Brm-associated factor subunit ABRG1-associated factor 60ASWI/SNF complex 60 kDa subunit ASwp73-like proteinchromatin remodeling complex BAF60A scalcium-transporting ATPase type 2C member 2ATPase 2C2ATPase, Ca++ transporting, type 2C, member 2secretory pathway Ca(2+)-ATPase 2secretory pathway calcium ATPase 2
Modification date2018052220180523
UniProtAcc

Q96GM5

O75185

Ensembl transtripts involved in fusion geneENST00000394963, ENST00000381513, 
ENST00000548573, ENST00000549526, 
ENST00000262429, ENST00000416219, 
ENST00000420010, 
Fusion gene scores* DoF score1 X 1 X 1=13 X 5 X 2=30
# samples 15
** MAII scorelog2(1/1*10)=3.32192809488736log2(5/30*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: SMARCD1 [Title/Abstract] AND ATP2C2 [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
HgeneSMARCD1

GO:0006337

nucleosome disassembly

8895581

HgeneSMARCD1

GO:0006338

chromatin remodeling

11726552


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
ChiTaRS3.1AW389291SMARCD1chr12

50484310

+ATP2C2chr16

84456272

+
* 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
Frame-shitENST00000394963ENST00000262429SMARCD1chr12

50484310

+ATP2C2chr16

84456272

+
Frame-shitENST00000394963ENST00000416219SMARCD1chr12

50484310

+ATP2C2chr16

84456272

+
5CDS-3UTRENST00000394963ENST00000420010SMARCD1chr12

50484310

+ATP2C2chr16

84456272

+
Frame-shitENST00000381513ENST00000262429SMARCD1chr12

50484310

+ATP2C2chr16

84456272

+
Frame-shitENST00000381513ENST00000416219SMARCD1chr12

50484310

+ATP2C2chr16

84456272

+
5CDS-3UTRENST00000381513ENST00000420010SMARCD1chr12

50484310

+ATP2C2chr16

84456272

+
Frame-shitENST00000548573ENST00000262429SMARCD1chr12

50484310

+ATP2C2chr16

84456272

+
Frame-shitENST00000548573ENST00000416219SMARCD1chr12

50484310

+ATP2C2chr16

84456272

+
5CDS-3UTRENST00000548573ENST00000420010SMARCD1chr12

50484310

+ATP2C2chr16

84456272

+
intron-3CDSENST00000549526ENST00000262429SMARCD1chr12

50484310

+ATP2C2chr16

84456272

+
intron-3CDSENST00000549526ENST00000416219SMARCD1chr12

50484310

+ATP2C2chr16

84456272

+
intron-3UTRENST00000549526ENST00000420010SMARCD1chr12

50484310

+ATP2C2chr16

84456272

+

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FusionProtFeatures for SMARCD1_ATP2C2


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
SMARCD1

Q96GM5

ATP2C2

O75185

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 (PubMed:8804307). 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 (By similarity). Has a stronginfluence on vitamin D-mediated transcriptional activity from anenhancer vitamin D receptor element (VDRE). May be a link betweenmammalian SWI-SNF-like chromatin remodeling complexes and thevitamin D receptor (VDR) heterodimer (PubMed:14698202). Mediatescritical interactions between nuclear receptors and theBRG1/SMARCA4 chromatin-remodeling complex for transactivation(PubMed:12917342). {ECO:0000250|UniProtKB:Q61466,ECO:0000269|PubMed:12917342, ECO:0000269|PubMed:14698202,ECO:0000269|PubMed:8804307, ECO:0000303|PubMed:22952240,ECO:0000303|PubMed:26601204}. This magnesium-dependent enzyme catalyzes the hydrolysisof ATP coupled with the transport of calcium. {ECO:0000250}.

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 SMARCD1_ATP2C2


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 SMARCD1_ATP2C2


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 SMARCD1_ATP2C2


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 SMARCD1_ATP2C2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource