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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:SCP2-ECHDC2 (FusionGDB2 ID:79233)

Fusion Gene Summary for SCP2-ECHDC2

check button Fusion gene summary
Fusion gene informationFusion gene name: SCP2-ECHDC2
Fusion gene ID: 79233
HgeneTgene
Gene symbol

SCP2

ECHDC2

Gene ID

10388

55268

Gene namesynaptonemal complex protein 2enoyl-CoA hydratase domain containing 2
SynonymsSCP-2|SCP2|SPGF1-
Cytomap

20q13.33

1p32.3

Type of geneprotein-codingprotein-coding
Descriptionsynaptonemal complex protein 2synaptonemal complex lateral element proteinenoyl-CoA hydratase domain-containing protein 2, mitochondrialenoyl Coenzyme A hydratase domain containing 2
Modification date2020031320200313
UniProtAcc.

Q86YB7

Ensembl transtripts involved in fusion geneENST00000371514, ENST00000528311, 
ENST00000371509, ENST00000407246, 
ENST00000371513, ENST00000473584, 
ENST00000430330, ENST00000408941, 
ENST00000435345, ENST00000488965, 
ENST00000371522, ENST00000358358, 
ENST00000536120, ENST00000541281, 
ENST00000480312, 
Fusion gene scores* DoF score9 X 8 X 4=2886 X 5 X 4=120
# samples 96
** MAII scorelog2(9/288*10)=-1.67807190511264
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/120*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SCP2 [Title/Abstract] AND ECHDC2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSCP2(53393137)-ECHDC2(53364896), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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

check buttonFusion gene breakpoints across SCP2 (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 ECHDC2 (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-E2-A1IH-01ASCP2chr1

53393137

-ECHDC2chr1

53364896

-


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Fusion Gene ORF analysis for SCP2-ECHDC2

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
In-frameENST00000371514ENST00000371522SCP2chr1

53393137

-ECHDC2chr1

53364896

-
In-frameENST00000371514ENST00000358358SCP2chr1

53393137

-ECHDC2chr1

53364896

-
In-frameENST00000371514ENST00000536120SCP2chr1

53393137

-ECHDC2chr1

53364896

-
5CDS-intronENST00000371514ENST00000541281SCP2chr1

53393137

-ECHDC2chr1

53364896

-
5CDS-intronENST00000371514ENST00000480312SCP2chr1

53393137

-ECHDC2chr1

53364896

-
5UTR-3CDSENST00000528311ENST00000371522SCP2chr1

53393137

-ECHDC2chr1

53364896

-
5UTR-3CDSENST00000528311ENST00000358358SCP2chr1

53393137

-ECHDC2chr1

53364896

-
5UTR-3CDSENST00000528311ENST00000536120SCP2chr1

53393137

-ECHDC2chr1

53364896

-
5UTR-intronENST00000528311ENST00000541281SCP2chr1

53393137

-ECHDC2chr1

53364896

-
5UTR-intronENST00000528311ENST00000480312SCP2chr1

53393137

-ECHDC2chr1

53364896

-
In-frameENST00000371509ENST00000371522SCP2chr1

53393137

-ECHDC2chr1

53364896

-
In-frameENST00000371509ENST00000358358SCP2chr1

53393137

-ECHDC2chr1

53364896

-
In-frameENST00000371509ENST00000536120SCP2chr1

53393137

-ECHDC2chr1

53364896

-
5CDS-intronENST00000371509ENST00000541281SCP2chr1

53393137

-ECHDC2chr1

53364896

-
5CDS-intronENST00000371509ENST00000480312SCP2chr1

53393137

-ECHDC2chr1

53364896

-
In-frameENST00000407246ENST00000371522SCP2chr1

53393137

-ECHDC2chr1

53364896

-
In-frameENST00000407246ENST00000358358SCP2chr1

53393137

-ECHDC2chr1

53364896

-
In-frameENST00000407246ENST00000536120SCP2chr1

53393137

-ECHDC2chr1

53364896

-
5CDS-intronENST00000407246ENST00000541281SCP2chr1

53393137

-ECHDC2chr1

53364896

-
5CDS-intronENST00000407246ENST00000480312SCP2chr1

53393137

-ECHDC2chr1

53364896

-
In-frameENST00000371513ENST00000371522SCP2chr1

53393137

-ECHDC2chr1

53364896

-
In-frameENST00000371513ENST00000358358SCP2chr1

53393137

-ECHDC2chr1

53364896

-
In-frameENST00000371513ENST00000536120SCP2chr1

53393137

-ECHDC2chr1

53364896

-
5CDS-intronENST00000371513ENST00000541281SCP2chr1

53393137

-ECHDC2chr1

53364896

-
5CDS-intronENST00000371513ENST00000480312SCP2chr1

53393137

-ECHDC2chr1

53364896

-
intron-3CDSENST00000473584ENST00000371522SCP2chr1

53393137

-ECHDC2chr1

53364896

-
intron-3CDSENST00000473584ENST00000358358SCP2chr1

53393137

-ECHDC2chr1

53364896

-
intron-3CDSENST00000473584ENST00000536120SCP2chr1

53393137

-ECHDC2chr1

53364896

-
intron-intronENST00000473584ENST00000541281SCP2chr1

53393137

-ECHDC2chr1

53364896

-
intron-intronENST00000473584ENST00000480312SCP2chr1

53393137

-ECHDC2chr1

53364896

-
intron-3CDSENST00000430330ENST00000371522SCP2chr1

53393137

-ECHDC2chr1

53364896

-
intron-3CDSENST00000430330ENST00000358358SCP2chr1

53393137

-ECHDC2chr1

53364896

-
intron-3CDSENST00000430330ENST00000536120SCP2chr1

53393137

-ECHDC2chr1

53364896

-
intron-intronENST00000430330ENST00000541281SCP2chr1

53393137

-ECHDC2chr1

53364896

-
intron-intronENST00000430330ENST00000480312SCP2chr1

53393137

-ECHDC2chr1

53364896

-
intron-3CDSENST00000408941ENST00000371522SCP2chr1

53393137

-ECHDC2chr1

53364896

-
intron-3CDSENST00000408941ENST00000358358SCP2chr1

53393137

-ECHDC2chr1

53364896

-
intron-3CDSENST00000408941ENST00000536120SCP2chr1

53393137

-ECHDC2chr1

53364896

-
intron-intronENST00000408941ENST00000541281SCP2chr1

53393137

-ECHDC2chr1

53364896

-
intron-intronENST00000408941ENST00000480312SCP2chr1

53393137

-ECHDC2chr1

53364896

-
intron-3CDSENST00000435345ENST00000371522SCP2chr1

53393137

-ECHDC2chr1

53364896

-
intron-3CDSENST00000435345ENST00000358358SCP2chr1

53393137

-ECHDC2chr1

53364896

-
intron-3CDSENST00000435345ENST00000536120SCP2chr1

53393137

-ECHDC2chr1

53364896

-
intron-intronENST00000435345ENST00000541281SCP2chr1

53393137

-ECHDC2chr1

53364896

-
intron-intronENST00000435345ENST00000480312SCP2chr1

53393137

-ECHDC2chr1

53364896

-
intron-3CDSENST00000488965ENST00000371522SCP2chr1

53393137

-ECHDC2chr1

53364896

-
intron-3CDSENST00000488965ENST00000358358SCP2chr1

53393137

-ECHDC2chr1

53364896

-
intron-3CDSENST00000488965ENST00000536120SCP2chr1

53393137

-ECHDC2chr1

53364896

-
intron-intronENST00000488965ENST00000541281SCP2chr1

53393137

-ECHDC2chr1

53364896

-
intron-intronENST00000488965ENST00000480312SCP2chr1

53393137

-ECHDC2chr1

53364896

-

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-ECHDC2


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 SCP2-ECHDC2


check button Go to

FGviewer for the breakpoints of chr1:53393137-chr1:53364896

.
- 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
.ECHDC2

Q86YB7

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.

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
HgeneSCP2chr1:53393137chr1:53364896ENST00000371509-115433_54323.0504.0DomainNote=SCP2
HgeneSCP2chr1:53393137chr1:53364896ENST00000371513-111433_54323.0323.0DomainNote=SCP2
HgeneSCP2chr1:53393137chr1:53364896ENST00000371514-116433_54323.0548.0DomainNote=SCP2
HgeneSCP2chr1:53393137chr1:53364896ENST00000407246-115433_54323.0524.0DomainNote=SCP2
HgeneSCP2chr1:53393137chr1:53364896ENST00000408941-14433_5430361.0DomainNote=SCP2
HgeneSCP2chr1:53393137chr1:53364896ENST00000430330-15433_5430141.0DomainNote=SCP2
HgeneSCP2chr1:53393137chr1:53364896ENST00000435345-15433_5430144.0DomainNote=SCP2
HgeneSCP2chr1:53393137chr1:53364896ENST00000488965-13433_543060.0DomainNote=SCP2
HgeneSCP2chr1:53393137chr1:53364896ENST00000528311-115433_5430467.0DomainNote=SCP2
HgeneSCP2chr1:53393137chr1:53364896ENST00000371509-115545_54723.0504.0MotifMicrobody targeting signal
HgeneSCP2chr1:53393137chr1:53364896ENST00000371513-111545_54723.0323.0MotifMicrobody targeting signal
HgeneSCP2chr1:53393137chr1:53364896ENST00000371514-116545_54723.0548.0MotifMicrobody targeting signal
HgeneSCP2chr1:53393137chr1:53364896ENST00000407246-115545_54723.0524.0MotifMicrobody targeting signal
HgeneSCP2chr1:53393137chr1:53364896ENST00000408941-14545_5470361.0MotifMicrobody targeting signal
HgeneSCP2chr1:53393137chr1:53364896ENST00000430330-15545_5470141.0MotifMicrobody targeting signal
HgeneSCP2chr1:53393137chr1:53364896ENST00000435345-15545_5470144.0MotifMicrobody targeting signal
HgeneSCP2chr1:53393137chr1:53364896ENST00000488965-13545_547060.0MotifMicrobody targeting signal
HgeneSCP2chr1:53393137chr1:53364896ENST00000528311-115545_5470467.0MotifMicrobody targeting signal


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Fusion Gene Sequence for SCP2-ECHDC2


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-ECHDC2


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-ECHDC2


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-ECHDC2


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