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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:SMARCD2-HCK (FusionGDB2 ID:83969)

Fusion Gene Summary for SMARCD2-HCK

check button Fusion gene summary
Fusion gene informationFusion gene name: SMARCD2-HCK
Fusion gene ID: 83969
HgeneTgene
Gene symbol

SMARCD2

HCK

Gene ID

6603

3055

Gene nameSWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2HCK proto-oncogene, Src family tyrosine kinase
SynonymsBAF60B|CRACD2|PRO2451|Rsc6p|SGD2JTK9|p59Hck|p61Hck
Cytomap

17q23.3

20q11.21

Type of geneprotein-codingprotein-coding
DescriptionSWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 260 kDa BRG-1/Brm-associated factor subunit BBRG1-associated factor 60BSWI/SNF complex 60 kDa subunit BSwp73-like proteinchromatin remodeling complex BAF60B styrosine-protein kinase HCKhematopoietic cell kinasehemopoietic cell kinasep59-HCK/p60-HCK
Modification date2020031320200329
UniProtAcc.

P08631

Ensembl transtripts involved in fusion geneENST00000448276, ENST00000225742, 
ENST00000323347, 		ENST00000375852, 
ENST00000375862, ENST00000518730, 
ENST00000520553, ENST00000538448, 
ENST00000534862, 
Fusion gene scores* DoF score5 X 9 X 4=18010 X 10 X 7=700
# samples 814
** MAII scorelog2(8/180*10)=-1.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(14/700*10)=-2.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SMARCD2 [Title/Abstract] AND HCK [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSMARCD2(61919741)-HCK(30659465), # samples:1
SMARCD2(61919818)-HCK(30659464), # samples:1
SMARCD2(61919819)-HCK(30659465), # samples:1
Anticipated loss of major functional domain due to fusion event.SMARCD2-HCK seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
SMARCD2-HCK seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
SMARCD2-HCK seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
SMARCD2-HCK seems lost the major protein functional domain in Tgene partner, which is a kinase due to the frame-shifted ORF.
* 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
HgeneSMARCD2

GO:0006337

nucleosome disassembly

8895581

HgeneSMARCD2

GO:0006338

chromatin remodeling

11726552

TgeneHCK

GO:0071801

regulation of podosome assembly

15998323

TgeneHCK

GO:2000251

positive regulation of actin cytoskeleton reorganization

15998323


check buttonFusion gene breakpoints across SMARCD2 (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 HCK (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
ChimerDB4BRCATCGA-C8-A273-01ASMARCD2chr17

61919741

-HCKchr20

30659465

+
ChimerDB4BRCATCGA-C8-A273-01ASMARCD2chr17

61919819

-HCKchr20

30659465

+
ChimerDB4BRCATCGA-C8-A273SMARCD2chr17

61919818

-HCKchr20

30659464

+


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Fusion Gene ORF analysis for SMARCD2-HCK

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-5UTRENST00000448276ENST00000375852SMARCD2chr17

61919819

-HCKchr20

30659465

+
5CDS-5UTRENST00000448276ENST00000375852SMARCD2chr17

61919818

-HCKchr20

30659464

+
5CDS-5UTRENST00000448276ENST00000375862SMARCD2chr17

61919819

-HCKchr20

30659465

+
5CDS-5UTRENST00000448276ENST00000375862SMARCD2chr17

61919818

-HCKchr20

30659464

+
5CDS-5UTRENST00000448276ENST00000518730SMARCD2chr17

61919819

-HCKchr20

30659465

+
5CDS-5UTRENST00000448276ENST00000518730SMARCD2chr17

61919818

-HCKchr20

30659464

+
5CDS-5UTRENST00000448276ENST00000520553SMARCD2chr17

61919819

-HCKchr20

30659465

+
5CDS-5UTRENST00000448276ENST00000520553SMARCD2chr17

61919818

-HCKchr20

30659464

+
5CDS-5UTRENST00000448276ENST00000538448SMARCD2chr17

61919819

-HCKchr20

30659465

+
5CDS-5UTRENST00000448276ENST00000538448SMARCD2chr17

61919818

-HCKchr20

30659464

+
5UTR-3CDSENST00000225742ENST00000534862SMARCD2chr17

61919741

-HCKchr20

30659465

+
5UTR-5UTRENST00000225742ENST00000375852SMARCD2chr17

61919741

-HCKchr20

30659465

+
5UTR-5UTRENST00000225742ENST00000375862SMARCD2chr17

61919741

-HCKchr20

30659465

+
5UTR-5UTRENST00000225742ENST00000518730SMARCD2chr17

61919741

-HCKchr20

30659465

+
5UTR-5UTRENST00000225742ENST00000520553SMARCD2chr17

61919741

-HCKchr20

30659465

+
5UTR-5UTRENST00000225742ENST00000538448SMARCD2chr17

61919741

-HCKchr20

30659465

+
Frame-shiftENST00000448276ENST00000534862SMARCD2chr17

61919819

-HCKchr20

30659465

+
Frame-shiftENST00000448276ENST00000534862SMARCD2chr17

61919818

-HCKchr20

30659464

+
intron-3CDSENST00000225742ENST00000534862SMARCD2chr17

61919819

-HCKchr20

30659465

+
intron-3CDSENST00000225742ENST00000534862SMARCD2chr17

61919818

-HCKchr20

30659464

+
intron-3CDSENST00000323347ENST00000534862SMARCD2chr17

61919741

-HCKchr20

30659465

+
intron-3CDSENST00000323347ENST00000534862SMARCD2chr17

61919819

-HCKchr20

30659465

+
intron-3CDSENST00000323347ENST00000534862SMARCD2chr17

61919818

-HCKchr20

30659464

+
intron-3CDSENST00000448276ENST00000534862SMARCD2chr17

61919741

-HCKchr20

30659465

+
intron-5UTRENST00000225742ENST00000375852SMARCD2chr17

61919819

-HCKchr20

30659465

+
intron-5UTRENST00000225742ENST00000375852SMARCD2chr17

61919818

-HCKchr20

30659464

+
intron-5UTRENST00000225742ENST00000375862SMARCD2chr17

61919819

-HCKchr20

30659465

+
intron-5UTRENST00000225742ENST00000375862SMARCD2chr17

61919818

-HCKchr20

30659464

+
intron-5UTRENST00000225742ENST00000518730SMARCD2chr17

61919819

-HCKchr20

30659465

+
intron-5UTRENST00000225742ENST00000518730SMARCD2chr17

61919818

-HCKchr20

30659464

+
intron-5UTRENST00000225742ENST00000520553SMARCD2chr17

61919819

-HCKchr20

30659465

+
intron-5UTRENST00000225742ENST00000520553SMARCD2chr17

61919818

-HCKchr20

30659464

+
intron-5UTRENST00000225742ENST00000538448SMARCD2chr17

61919819

-HCKchr20

30659465

+
intron-5UTRENST00000225742ENST00000538448SMARCD2chr17

61919818

-HCKchr20

30659464

+
intron-5UTRENST00000323347ENST00000375852SMARCD2chr17

61919741

-HCKchr20

30659465

+
intron-5UTRENST00000323347ENST00000375852SMARCD2chr17

61919819

-HCKchr20

30659465

+
intron-5UTRENST00000323347ENST00000375852SMARCD2chr17

61919818

-HCKchr20

30659464

+
intron-5UTRENST00000323347ENST00000375862SMARCD2chr17

61919741

-HCKchr20

30659465

+
intron-5UTRENST00000323347ENST00000375862SMARCD2chr17

61919819

-HCKchr20

30659465

+
intron-5UTRENST00000323347ENST00000375862SMARCD2chr17

61919818

-HCKchr20

30659464

+
intron-5UTRENST00000323347ENST00000518730SMARCD2chr17

61919741

-HCKchr20

30659465

+
intron-5UTRENST00000323347ENST00000518730SMARCD2chr17

61919819

-HCKchr20

30659465

+
intron-5UTRENST00000323347ENST00000518730SMARCD2chr17

61919818

-HCKchr20

30659464

+
intron-5UTRENST00000323347ENST00000520553SMARCD2chr17

61919741

-HCKchr20

30659465

+
intron-5UTRENST00000323347ENST00000520553SMARCD2chr17

61919819

-HCKchr20

30659465

+
intron-5UTRENST00000323347ENST00000520553SMARCD2chr17

61919818

-HCKchr20

30659464

+
intron-5UTRENST00000323347ENST00000538448SMARCD2chr17

61919741

-HCKchr20

30659465

+
intron-5UTRENST00000323347ENST00000538448SMARCD2chr17

61919819

-HCKchr20

30659465

+
intron-5UTRENST00000323347ENST00000538448SMARCD2chr17

61919818

-HCKchr20

30659464

+
intron-5UTRENST00000448276ENST00000375852SMARCD2chr17

61919741

-HCKchr20

30659465

+
intron-5UTRENST00000448276ENST00000375862SMARCD2chr17

61919741

-HCKchr20

30659465

+
intron-5UTRENST00000448276ENST00000518730SMARCD2chr17

61919741

-HCKchr20

30659465

+
intron-5UTRENST00000448276ENST00000520553SMARCD2chr17

61919741

-HCKchr20

30659465

+
intron-5UTRENST00000448276ENST00000538448SMARCD2chr17

61919741

-HCKchr20

30659465

+

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 SMARCD2-HCK


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)
SMARCD2chr1761919740-HCKchr2030659464+0.0031728540.99682707
SMARCD2chr1761919818-HCKchr2030659464+0.0024718580.99752814
SMARCD2chr1761919818-HCKchr2030659464+0.0024718580.99752814
SMARCD2chr1761919740-HCKchr2030659464+0.0031728540.99682707
SMARCD2chr1761919818-HCKchr2030659464+0.0024718580.99752814
SMARCD2chr1761919818-HCKchr2030659464+0.0024718580.99752814

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.
genomic feature of top 1%

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Fusion Protein Features for SMARCD2-HCK


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:61919741/:30659465)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

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

P08631

FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is 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, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Non-receptor tyrosine-protein kinase found in hematopoietic cells that transmits signals from cell surface receptors and plays an important role in the regulation of innate immune responses, including neutrophil, monocyte, macrophage and mast cell functions, phagocytosis, cell survival and proliferation, cell adhesion and migration. Acts downstream of receptors that bind the Fc region of immunoglobulins, such as FCGR1A and FCGR2A, but also CSF3R, PLAUR, the receptors for IFNG, IL2, IL6 and IL8, and integrins, such as ITGB1 and ITGB2. During the phagocytic process, mediates mobilization of secretory lysosomes, degranulation, and activation of NADPH oxidase to bring about the respiratory burst. Plays a role in the release of inflammatory molecules. Promotes reorganization of the actin cytoskeleton and actin polymerization, formation of podosomes and cell protrusions. Inhibits TP73-mediated transcription activation and TP73-mediated apoptosis. Phosphorylates CBL in response to activation of immunoglobulin gamma Fc region receptors. Phosphorylates ADAM15, BCR, ELMO1, FCGR2A, GAB1, GAB2, RAPGEF1, STAT5B, TP73, VAV1 and WAS. {ECO:0000269|PubMed:10092522, ECO:0000269|PubMed:10779760, ECO:0000269|PubMed:10973280, ECO:0000269|PubMed:11741929, ECO:0000269|PubMed:11896602, ECO:0000269|PubMed:12411494, ECO:0000269|PubMed:15010462, ECO:0000269|PubMed:15952790, ECO:0000269|PubMed:15998323, ECO:0000269|PubMed:17310994, ECO:0000269|PubMed:17535448, ECO:0000269|PubMed:19114024, ECO:0000269|PubMed:19903482, ECO:0000269|PubMed:20452982, ECO:0000269|PubMed:21338576, ECO:0000269|PubMed:7535819, ECO:0000269|PubMed:8132624, ECO:0000269|PubMed:9406996, ECO:0000269|PubMed:9407116}.

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 SMARCD2-HCK


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 SMARCD2-HCK


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 SMARCD2-HCK


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 SMARCD2-HCK


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