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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:SCP2-NCAM1 (FusionGDB2 ID:HG6342TG4684)

Fusion Gene Summary for SCP2-NCAM1

check button Fusion gene summary
Fusion gene informationFusion gene name: SCP2-NCAM1
Fusion gene ID: hg6342tg4684
HgeneTgene
Gene symbol

SCP2

NCAM1

Gene ID

6342

4684

Gene namesterol carrier protein 2neural cell adhesion molecule 1
SynonymsNLTP|NSL-TP|SCP-2|SCP-CHI|SCP-X|SCPXCD56|MSK39|NCAM
Cytomap('SCP2')('NCAM1')

1p32.3

11q23.2

Type of geneprotein-codingprotein-coding
Descriptionnon-specific lipid-transfer proteinepididymis secretory sperm binding proteinpropanoyl-CoA C-acyltransferasesterol carrier protein Xneural cell adhesion molecule 1antigen recognized by monoclonal antibody 5.1H11neural cell adhesion molecule, NCAM
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000371509, ENST00000371513, 
ENST00000371514, ENST00000407246, 
ENST00000528311, ENST00000408941, 
ENST00000430330, ENST00000435345, 
ENST00000473584, ENST00000488965, 
Fusion gene scores* DoF score9 X 8 X 4=28811 X 12 X 4=528
# samples 912
** MAII scorelog2(9/288*10)=-1.67807190511264
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(12/528*10)=-2.13750352374993
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SCP2 [Title/Abstract] AND NCAM1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSCP2(53393137)-NCAM1(113126596), # samples:1
SCP2(53393137)-NCAM1(113126599), # samples:1
Anticipated loss of major functional domain due to fusion event.SCP2-NCAM1 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
SCP2-NCAM1 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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
HgeneSCP2

GO:0032385

positive regulation of intracellular cholesterol transport

15449949

HgeneSCP2

GO:1901373

lipid hydroperoxide transport

15449949



check button Fusion gene information
* 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
ChimerDB4PRADTCGA-V1-A9ZG-01ASCP2chr1

53393137

+NCAM1chr11

113126596

+
ChimerDB4PRADTCGA-V1-A9ZG-01ASCP2chr1

53393137

-NCAM1chr11

113126599

+


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Fusion Gene ORF analysis for SCP2-NCAM1

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-3UTRENST00000371509ENST00000316851SCP2chr1

53393137

+NCAM1chr11

113126596

+
5CDS-3UTRENST00000371509ENST00000316851SCP2chr1

53393137

-NCAM1chr11

113126599

+
5CDS-3UTRENST00000371509ENST00000397957SCP2chr1

53393137

+NCAM1chr11

113126596

+
5CDS-3UTRENST00000371509ENST00000397957SCP2chr1

53393137

-NCAM1chr11

113126599

+
5CDS-3UTRENST00000371513ENST00000316851SCP2chr1

53393137

+NCAM1chr11

113126596

+
5CDS-3UTRENST00000371513ENST00000316851SCP2chr1

53393137

-NCAM1chr11

113126599

+
5CDS-3UTRENST00000371513ENST00000397957SCP2chr1

53393137

+NCAM1chr11

113126596

+
5CDS-3UTRENST00000371513ENST00000397957SCP2chr1

53393137

-NCAM1chr11

113126599

+
5CDS-3UTRENST00000371514ENST00000316851SCP2chr1

53393137

+NCAM1chr11

113126596

+
5CDS-3UTRENST00000371514ENST00000316851SCP2chr1

53393137

-NCAM1chr11

113126599

+
5CDS-3UTRENST00000371514ENST00000397957SCP2chr1

53393137

+NCAM1chr11

113126596

+
5CDS-3UTRENST00000371514ENST00000397957SCP2chr1

53393137

-NCAM1chr11

113126599

+
5CDS-3UTRENST00000407246ENST00000316851SCP2chr1

53393137

+NCAM1chr11

113126596

+
5CDS-3UTRENST00000407246ENST00000316851SCP2chr1

53393137

-NCAM1chr11

113126599

+
5CDS-3UTRENST00000407246ENST00000397957SCP2chr1

53393137

+NCAM1chr11

113126596

+
5CDS-3UTRENST00000407246ENST00000397957SCP2chr1

53393137

-NCAM1chr11

113126599

+
5CDS-intronENST00000371509ENST00000401611SCP2chr1

53393137

+NCAM1chr11

113126596

+
5CDS-intronENST00000371509ENST00000401611SCP2chr1

53393137

-NCAM1chr11

113126599

+
5CDS-intronENST00000371513ENST00000401611SCP2chr1

53393137

+NCAM1chr11

113126596

+
5CDS-intronENST00000371513ENST00000401611SCP2chr1

53393137

-NCAM1chr11

113126599

+
5CDS-intronENST00000371514ENST00000401611SCP2chr1

53393137

+NCAM1chr11

113126596

+
5CDS-intronENST00000371514ENST00000401611SCP2chr1

53393137

-NCAM1chr11

113126599

+
5CDS-intronENST00000407246ENST00000401611SCP2chr1

53393137

+NCAM1chr11

113126596

+
5CDS-intronENST00000407246ENST00000401611SCP2chr1

53393137

-NCAM1chr11

113126599

+
5UTR-3CDSENST00000528311ENST00000533760SCP2chr1

53393137

+NCAM1chr11

113126596

+
5UTR-3CDSENST00000528311ENST00000533760SCP2chr1

53393137

-NCAM1chr11

113126599

+
5UTR-3UTRENST00000528311ENST00000316851SCP2chr1

53393137

+NCAM1chr11

113126596

+
5UTR-3UTRENST00000528311ENST00000316851SCP2chr1

53393137

-NCAM1chr11

113126599

+
5UTR-3UTRENST00000528311ENST00000397957SCP2chr1

53393137

+NCAM1chr11

113126596

+
5UTR-3UTRENST00000528311ENST00000397957SCP2chr1

53393137

-NCAM1chr11

113126599

+
5UTR-intronENST00000528311ENST00000401611SCP2chr1

53393137

+NCAM1chr11

113126596

+
5UTR-intronENST00000528311ENST00000401611SCP2chr1

53393137

-NCAM1chr11

113126599

+
Frame-shiftENST00000371509ENST00000533760SCP2chr1

53393137

+NCAM1chr11

113126596

+
Frame-shiftENST00000371509ENST00000533760SCP2chr1

53393137

-NCAM1chr11

113126599

+
Frame-shiftENST00000371513ENST00000533760SCP2chr1

53393137

+NCAM1chr11

113126596

+
Frame-shiftENST00000371513ENST00000533760SCP2chr1

53393137

-NCAM1chr11

113126599

+
Frame-shiftENST00000371514ENST00000533760SCP2chr1

53393137

+NCAM1chr11

113126596

+
Frame-shiftENST00000371514ENST00000533760SCP2chr1

53393137

-NCAM1chr11

113126599

+
Frame-shiftENST00000407246ENST00000533760SCP2chr1

53393137

+NCAM1chr11

113126596

+
Frame-shiftENST00000407246ENST00000533760SCP2chr1

53393137

-NCAM1chr11

113126599

+
intron-3CDSENST00000408941ENST00000533760SCP2chr1

53393137

+NCAM1chr11

113126596

+
intron-3CDSENST00000408941ENST00000533760SCP2chr1

53393137

-NCAM1chr11

113126599

+
intron-3CDSENST00000430330ENST00000533760SCP2chr1

53393137

+NCAM1chr11

113126596

+
intron-3CDSENST00000430330ENST00000533760SCP2chr1

53393137

-NCAM1chr11

113126599

+
intron-3CDSENST00000435345ENST00000533760SCP2chr1

53393137

+NCAM1chr11

113126596

+
intron-3CDSENST00000435345ENST00000533760SCP2chr1

53393137

-NCAM1chr11

113126599

+
intron-3CDSENST00000473584ENST00000533760SCP2chr1

53393137

+NCAM1chr11

113126596

+
intron-3CDSENST00000473584ENST00000533760SCP2chr1

53393137

-NCAM1chr11

113126599

+
intron-3CDSENST00000488965ENST00000533760SCP2chr1

53393137

+NCAM1chr11

113126596

+
intron-3CDSENST00000488965ENST00000533760SCP2chr1

53393137

-NCAM1chr11

113126599

+
intron-3UTRENST00000408941ENST00000316851SCP2chr1

53393137

+NCAM1chr11

113126596

+
intron-3UTRENST00000408941ENST00000316851SCP2chr1

53393137

-NCAM1chr11

113126599

+
intron-3UTRENST00000408941ENST00000397957SCP2chr1

53393137

+NCAM1chr11

113126596

+
intron-3UTRENST00000408941ENST00000397957SCP2chr1

53393137

-NCAM1chr11

113126599

+
intron-3UTRENST00000430330ENST00000316851SCP2chr1

53393137

+NCAM1chr11

113126596

+
intron-3UTRENST00000430330ENST00000316851SCP2chr1

53393137

-NCAM1chr11

113126599

+
intron-3UTRENST00000430330ENST00000397957SCP2chr1

53393137

+NCAM1chr11

113126596

+
intron-3UTRENST00000430330ENST00000397957SCP2chr1

53393137

-NCAM1chr11

113126599

+
intron-3UTRENST00000435345ENST00000316851SCP2chr1

53393137

+NCAM1chr11

113126596

+
intron-3UTRENST00000435345ENST00000316851SCP2chr1

53393137

-NCAM1chr11

113126599

+
intron-3UTRENST00000435345ENST00000397957SCP2chr1

53393137

+NCAM1chr11

113126596

+
intron-3UTRENST00000435345ENST00000397957SCP2chr1

53393137

-NCAM1chr11

113126599

+
intron-3UTRENST00000473584ENST00000316851SCP2chr1

53393137

+NCAM1chr11

113126596

+
intron-3UTRENST00000473584ENST00000316851SCP2chr1

53393137

-NCAM1chr11

113126599

+
intron-3UTRENST00000473584ENST00000397957SCP2chr1

53393137

+NCAM1chr11

113126596

+
intron-3UTRENST00000473584ENST00000397957SCP2chr1

53393137

-NCAM1chr11

113126599

+
intron-3UTRENST00000488965ENST00000316851SCP2chr1

53393137

+NCAM1chr11

113126596

+
intron-3UTRENST00000488965ENST00000316851SCP2chr1

53393137

-NCAM1chr11

113126599

+
intron-3UTRENST00000488965ENST00000397957SCP2chr1

53393137

+NCAM1chr11

113126596

+
intron-3UTRENST00000488965ENST00000397957SCP2chr1

53393137

-NCAM1chr11

113126599

+
intron-intronENST00000408941ENST00000401611SCP2chr1

53393137

+NCAM1chr11

113126596

+
intron-intronENST00000408941ENST00000401611SCP2chr1

53393137

-NCAM1chr11

113126599

+
intron-intronENST00000430330ENST00000401611SCP2chr1

53393137

+NCAM1chr11

113126596

+
intron-intronENST00000430330ENST00000401611SCP2chr1

53393137

-NCAM1chr11

113126599

+
intron-intronENST00000435345ENST00000401611SCP2chr1

53393137

+NCAM1chr11

113126596

+
intron-intronENST00000435345ENST00000401611SCP2chr1

53393137

-NCAM1chr11

113126599

+
intron-intronENST00000473584ENST00000401611SCP2chr1

53393137

+NCAM1chr11

113126596

+
intron-intronENST00000473584ENST00000401611SCP2chr1

53393137

-NCAM1chr11

113126599

+
intron-intronENST00000488965ENST00000401611SCP2chr1

53393137

+NCAM1chr11

113126596

+
intron-intronENST00000488965ENST00000401611SCP2chr1

53393137

-NCAM1chr11

113126599

+

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 SCP2-NCAM1


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)
SCP2chr153393137+NCAM1chr11113126595+2.50E-101
SCP2chr153393137+NCAM1chr11113126595+2.50E-101


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 SCP2-NCAM1


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/:53393137/:113126596)
- 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
..
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: 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}.

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 SCP2-NCAM1


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 SCP2-NCAM1


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 SCP2-NCAM1


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 SCP2-NCAM1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSCP2C3150990LEUKOENCEPHALOPATHY WITH DYSTONIA AND MOTOR NEUROPATHY2CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneSCP2C0013421Dystonia1CTD_human
HgeneSCP2C0152025Polyneuropathy1CTD_human
HgeneSCP2C0270612Leukoencephalopathy1CTD_human
HgeneSCP2C0271683Polyneuropathy, Motor1CTD_human
HgeneSCP2C0393588Dystonia, Paroxysmal1CTD_human
HgeneSCP2C0393610Dystonia, Diurnal1CTD_human
HgeneSCP2C0393851Polyneuropathy, Critical Illness1CTD_human
HgeneSCP2C0751093Dystonia, Limb1CTD_human
HgeneSCP2C0751448Polyneuropathy, Familial1CTD_human
HgeneSCP2C0751449Acquired Polyneuropathy1CTD_human
HgeneSCP2C1858991Childhood Ataxia with Central Nervous System Hypomyelinization1CTD_human
TgeneC0005586Bipolar Disorder5PSYGENET
TgeneC0001973Alcoholic Intoxication, Chronic4PSYGENET
TgeneC0011570Mental Depression4PSYGENET
TgeneC0011581Depressive disorder4PSYGENET
TgeneC0036341Schizophrenia3PSYGENET
TgeneC0525045Mood Disorders2PSYGENET
TgeneC0000786Spontaneous abortion1CTD_human
TgeneC0000822Abortion, Tubal1CTD_human
TgeneC0005587Depression, Bipolar1PSYGENET
TgeneC0024809Marijuana Abuse1PSYGENET
TgeneC0027626Neoplasm Invasiveness1CTD_human
TgeneC0041696Unipolar Depression1PSYGENET
TgeneC1269683Major Depressive Disorder1PSYGENET
TgeneC3830362Early Pregnancy Loss1CTD_human
TgeneC4552766Miscarriage1CTD_human