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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:SAP130-BIN1 (FusionGDB2 ID:78646)

Fusion Gene Summary for SAP130-BIN1

check button Fusion gene summary
Fusion gene informationFusion gene name: SAP130-BIN1
Fusion gene ID: 78646
HgeneTgene
Gene symbol

SAP130

BIN1

Gene ID

79595

274

Gene nameSin3A associated protein 130bridging integrator 1
Synonyms-AMPH2|AMPHL|CNM2|SH3P9
Cytomap

2q14.3

2q14.3

Type of geneprotein-codingprotein-coding
Descriptionhistone deacetylase complex subunit SAP130130 kDa Sin3-associated polypeptideSin3-associated polypeptide p130Sin3A associated protein 130kDamyc box-dependent-interacting protein 1amphiphysin IIamphiphysin-like proteinbox dependant MYC interacting protein 1box-dependent myc-interacting protein 1
Modification date2020031320200322
UniProtAcc.

O00499

Ensembl transtripts involved in fusion geneENST00000357702, ENST00000259235, 
ENST00000259234, 		ENST00000376113, 
ENST00000346226, ENST00000352848, 
ENST00000393041, ENST00000348750, 
ENST00000357970, ENST00000259238, 
ENST00000393040, ENST00000351659, 
ENST00000316724, ENST00000409400, 
ENST00000466111, 
Fusion gene scores* DoF score3 X 3 X 2=188 X 8 X 4=256
# samples 38
** MAII scorelog2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(8/256*10)=-1.67807190511264
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SAP130 [Title/Abstract] AND BIN1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSAP130(128735559)-BIN1(127834282), # samples:2
Anticipated loss of major functional domain due to fusion event.SAP130-BIN1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
SAP130-BIN1 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
SAP130-BIN1 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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
TgeneBIN1

GO:0033292

T-tubule organization

24755653

TgeneBIN1

GO:0043065

positive regulation of apoptotic process

16530520

TgeneBIN1

GO:0071156

regulation of cell cycle arrest

10412034


check buttonFusion gene breakpoints across SAP130 (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 BIN1 (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
ChimerDB4SKCMTCGA-EB-A3XC-01ASAP130chr2

128735559

-BIN1chr2

127834282

-
ChimerDB4SKCMTCGA-EB-A3XC-01ASAP130chr2

128735559

-BIN1chr2

127834282

-


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Fusion Gene ORF analysis for SAP130-BIN1

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-shiftENST00000357702ENST00000376113SAP130chr2

128735559

-BIN1chr2

127834282

-
Frame-shiftENST00000357702ENST00000346226SAP130chr2

128735559

-BIN1chr2

127834282

-
Frame-shiftENST00000357702ENST00000352848SAP130chr2

128735559

-BIN1chr2

127834282

-
Frame-shiftENST00000357702ENST00000393041SAP130chr2

128735559

-BIN1chr2

127834282

-
Frame-shiftENST00000357702ENST00000348750SAP130chr2

128735559

-BIN1chr2

127834282

-
Frame-shiftENST00000357702ENST00000357970SAP130chr2

128735559

-BIN1chr2

127834282

-
Frame-shiftENST00000357702ENST00000259238SAP130chr2

128735559

-BIN1chr2

127834282

-
Frame-shiftENST00000357702ENST00000393040SAP130chr2

128735559

-BIN1chr2

127834282

-
Frame-shiftENST00000357702ENST00000351659SAP130chr2

128735559

-BIN1chr2

127834282

-
Frame-shiftENST00000357702ENST00000316724SAP130chr2

128735559

-BIN1chr2

127834282

-
Frame-shiftENST00000357702ENST00000409400SAP130chr2

128735559

-BIN1chr2

127834282

-
5CDS-intronENST00000357702ENST00000466111SAP130chr2

128735559

-BIN1chr2

127834282

-
intron-3CDSENST00000259235ENST00000376113SAP130chr2

128735559

-BIN1chr2

127834282

-
intron-3CDSENST00000259235ENST00000346226SAP130chr2

128735559

-BIN1chr2

127834282

-
intron-3CDSENST00000259235ENST00000352848SAP130chr2

128735559

-BIN1chr2

127834282

-
intron-3CDSENST00000259235ENST00000393041SAP130chr2

128735559

-BIN1chr2

127834282

-
intron-3CDSENST00000259235ENST00000348750SAP130chr2

128735559

-BIN1chr2

127834282

-
intron-3CDSENST00000259235ENST00000357970SAP130chr2

128735559

-BIN1chr2

127834282

-
intron-3CDSENST00000259235ENST00000259238SAP130chr2

128735559

-BIN1chr2

127834282

-
intron-3CDSENST00000259235ENST00000393040SAP130chr2

128735559

-BIN1chr2

127834282

-
intron-3CDSENST00000259235ENST00000351659SAP130chr2

128735559

-BIN1chr2

127834282

-
intron-3CDSENST00000259235ENST00000316724SAP130chr2

128735559

-BIN1chr2

127834282

-
intron-3CDSENST00000259235ENST00000409400SAP130chr2

128735559

-BIN1chr2

127834282

-
intron-intronENST00000259235ENST00000466111SAP130chr2

128735559

-BIN1chr2

127834282

-
Frame-shiftENST00000259234ENST00000376113SAP130chr2

128735559

-BIN1chr2

127834282

-
Frame-shiftENST00000259234ENST00000346226SAP130chr2

128735559

-BIN1chr2

127834282

-
Frame-shiftENST00000259234ENST00000352848SAP130chr2

128735559

-BIN1chr2

127834282

-
Frame-shiftENST00000259234ENST00000393041SAP130chr2

128735559

-BIN1chr2

127834282

-
Frame-shiftENST00000259234ENST00000348750SAP130chr2

128735559

-BIN1chr2

127834282

-
Frame-shiftENST00000259234ENST00000357970SAP130chr2

128735559

-BIN1chr2

127834282

-
Frame-shiftENST00000259234ENST00000259238SAP130chr2

128735559

-BIN1chr2

127834282

-
Frame-shiftENST00000259234ENST00000393040SAP130chr2

128735559

-BIN1chr2

127834282

-
Frame-shiftENST00000259234ENST00000351659SAP130chr2

128735559

-BIN1chr2

127834282

-
Frame-shiftENST00000259234ENST00000316724SAP130chr2

128735559

-BIN1chr2

127834282

-
Frame-shiftENST00000259234ENST00000409400SAP130chr2

128735559

-BIN1chr2

127834282

-
5CDS-intronENST00000259234ENST00000466111SAP130chr2

128735559

-BIN1chr2

127834282

-

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 SAP130-BIN1


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)

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.

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Fusion Protein Features for SAP130-BIN1


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.BIN1

O00499

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Is a key player in the control of plasma membrane curvature, membrane shaping and membrane remodeling. Required in muscle cells for the formation of T-tubules, tubular invaginations of the plasma membrane that function in depolarization-contraction coupling (PubMed:24755653). Is a negative regulator of endocytosis (By similarity). Is also involved in the regulation of intracellular vesicles sorting, modulation of BACE1 trafficking and the control of amyloid-beta production (PubMed:27179792). In neuronal circuits, endocytosis regulation may influence the internalization of PHF-tau aggregates (By similarity). May be involved in the regulation of MYC activity and the control cell proliferation (PubMed:8782822). Has actin bundling activity and stabilizes actin filaments against depolymerization in vitro (PubMed:28893863). {ECO:0000250|UniProtKB:O08839, ECO:0000269|PubMed:24755653, ECO:0000269|PubMed:27179792, ECO:0000269|PubMed:28893863, ECO:0000269|PubMed:8782822}.

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 SAP130-BIN1


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 SAP130-BIN1


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 SAP130-BIN1


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 SAP130-BIN1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSAP130C0152101Hypoplastic Left Heart Syndrome1CTD_human
TgeneBIN1C0410204Myopathy, Centronuclear, Autosomal Recessive4CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneBIN1C1834558Myopathy, Centronuclear, Autosomal Dominant2CTD_human;ORPHANET
TgeneBIN1C0002395Alzheimer's Disease1CTD_human
TgeneBIN1C0011265Presenile dementia1CTD_human
TgeneBIN1C0175709Centronuclear myopathy1CTD_human
TgeneBIN1C0234985Mental deterioration1CTD_human
TgeneBIN1C0276496Familial Alzheimer Disease (FAD)1CTD_human
TgeneBIN1C0338656Impaired cognition1CTD_human
TgeneBIN1C0410203X-linked centronuclear myopathy1CTD_human
TgeneBIN1C0410207Tubular Aggregate Myopathy1CTD_human
TgeneBIN1C0494463Alzheimer Disease, Late Onset1CTD_human
TgeneBIN1C0546126Acute Confusional Senile Dementia1CTD_human
TgeneBIN1C0546264Congenital Fiber Type Disproportion1CTD_human
TgeneBIN1C0750900Alzheimer's Disease, Focal Onset1CTD_human
TgeneBIN1C0750901Alzheimer Disease, Early Onset1CTD_human
TgeneBIN1C0752282Congenital Structural Myopathy1CTD_human
TgeneBIN1C1270972Mild cognitive disorder1CTD_human
TgeneBIN1C3645536Autosomal Recessive Centronuclear Myopathy1CTD_human;ORPHANET
TgeneBIN1C3661489Autosomal Dominant Myotubular Myopathy1CTD_human
TgeneBIN1C4551952Myopathy, Centronuclear, 11CTD_human