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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:NUMA1-CNTNAP3 (FusionGDB2 ID:60898)

Fusion Gene Summary for NUMA1-CNTNAP3

check button Fusion gene summary
Fusion gene informationFusion gene name: NUMA1-CNTNAP3
Fusion gene ID: 60898
HgeneTgene
Gene symbol

NUMA1

CNTNAP3

Gene ID

4926

79937

Gene namenuclear mitotic apparatus protein 1contactin associated protein family member 3
SynonymsNMP-22|NUMACASPR3|CNTNAP3A
Cytomap

11q13.4

9p12

Type of geneprotein-codingprotein-coding
Descriptionnuclear mitotic apparatus protein 1SP-H antigencentrophilin stabilizes mitotic spindle in mitotic cellsnuclear matrix protein-22structural nuclear proteincontactin-associated protein-like 3cell recognition molecule Caspr3contactin associated protein like 3
Modification date2020031320200329
UniProtAcc.

Q96NU0

Ensembl transtripts involved in fusion geneENST00000351960, ENST00000358965, 
ENST00000393695, ENST00000543450, 
ENST00000323947, ENST00000358144, 
ENST00000377653, ENST00000377659, 
ENST00000297668, ENST00000377656, 
Fusion gene scores* DoF score36 X 22 X 17=134643 X 3 X 3=27
# samples 433
** MAII scorelog2(43/13464*10)=-4.96862661174049
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: NUMA1 [Title/Abstract] AND CNTNAP3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNUMA1(71746948)-CNTNAP3(39074008), # samples:1
Anticipated loss of major functional domain due to fusion event.NUMA1-CNTNAP3 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
NUMA1-CNTNAP3 seems lost the major protein functional domain in Hgene partner, which is a essential gene 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
HgeneNUMA1

GO:0000132

establishment of mitotic spindle orientation

21816348

HgeneNUMA1

GO:0030953

astral microtubule organization

12445386

HgeneNUMA1

GO:0060236

regulation of mitotic spindle organization

26195665

HgeneNUMA1

GO:1902365

positive regulation of protein localization to spindle pole body

16076287


check buttonFusion gene breakpoints across NUMA1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across CNTNAP3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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-D3-A51E-06ANUMA1chr11

71746948

-CNTNAP3chr9

39074008

-


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Fusion Gene ORF analysis for NUMA1-CNTNAP3

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-intronENST00000351960ENST00000323947NUMA1chr11

71746948

-CNTNAP3chr9

39074008

-
5CDS-intronENST00000351960ENST00000358144NUMA1chr11

71746948

-CNTNAP3chr9

39074008

-
5CDS-intronENST00000351960ENST00000377653NUMA1chr11

71746948

-CNTNAP3chr9

39074008

-
5CDS-intronENST00000351960ENST00000377659NUMA1chr11

71746948

-CNTNAP3chr9

39074008

-
5CDS-intronENST00000358965ENST00000323947NUMA1chr11

71746948

-CNTNAP3chr9

39074008

-
5CDS-intronENST00000358965ENST00000358144NUMA1chr11

71746948

-CNTNAP3chr9

39074008

-
5CDS-intronENST00000358965ENST00000377653NUMA1chr11

71746948

-CNTNAP3chr9

39074008

-
5CDS-intronENST00000358965ENST00000377659NUMA1chr11

71746948

-CNTNAP3chr9

39074008

-
5CDS-intronENST00000393695ENST00000323947NUMA1chr11

71746948

-CNTNAP3chr9

39074008

-
5CDS-intronENST00000393695ENST00000358144NUMA1chr11

71746948

-CNTNAP3chr9

39074008

-
5CDS-intronENST00000393695ENST00000377653NUMA1chr11

71746948

-CNTNAP3chr9

39074008

-
5CDS-intronENST00000393695ENST00000377659NUMA1chr11

71746948

-CNTNAP3chr9

39074008

-
Frame-shiftENST00000351960ENST00000297668NUMA1chr11

71746948

-CNTNAP3chr9

39074008

-
Frame-shiftENST00000351960ENST00000377656NUMA1chr11

71746948

-CNTNAP3chr9

39074008

-
Frame-shiftENST00000358965ENST00000377656NUMA1chr11

71746948

-CNTNAP3chr9

39074008

-
Frame-shiftENST00000393695ENST00000297668NUMA1chr11

71746948

-CNTNAP3chr9

39074008

-
Frame-shiftENST00000393695ENST00000377656NUMA1chr11

71746948

-CNTNAP3chr9

39074008

-
In-frameENST00000358965ENST00000297668NUMA1chr11

71746948

-CNTNAP3chr9

39074008

-
intron-3CDSENST00000543450ENST00000297668NUMA1chr11

71746948

-CNTNAP3chr9

39074008

-
intron-3CDSENST00000543450ENST00000377656NUMA1chr11

71746948

-CNTNAP3chr9

39074008

-
intron-intronENST00000543450ENST00000323947NUMA1chr11

71746948

-CNTNAP3chr9

39074008

-
intron-intronENST00000543450ENST00000358144NUMA1chr11

71746948

-CNTNAP3chr9

39074008

-
intron-intronENST00000543450ENST00000377653NUMA1chr11

71746948

-CNTNAP3chr9

39074008

-
intron-intronENST00000543450ENST00000377659NUMA1chr11

71746948

-CNTNAP3chr9

39074008

-

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)
ENST00000358965NUMA1chr1171746948-ENST00000297668CNTNAP3chr939074008-154530015842187

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
ENST00000358965ENST00000297668NUMA1chr1171746948-CNTNAP3chr939074008-0.53374590.4662541

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Fusion Genomic Features for NUMA1-CNTNAP3


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.
genomic feature

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 NUMA1-CNTNAP3


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/chr11:71746948/chr9:39074008)
- 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
.CNTNAP3

Q96NU0

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
TgeneCNTNAP3chr11:71746948chr9:39074008ENST0000029766822241267_128812481289.0Topological domainCytoplasmic
TgeneCNTNAP3chr11:71746948chr9:39074008ENST0000029766822241246_126612481289.0TransmembraneHelical

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneNUMA1chr11:71746948chr9:39074008ENST00000358965-427213_1699142102.0Coiled coilOntology_term=ECO:0000255
HgeneNUMA1chr11:71746948chr9:39074008ENST00000393695-327213_1699142116.0Coiled coilOntology_term=ECO:0000255
HgeneNUMA1chr11:71746948chr9:39074008ENST00000358965-4271742_1748142102.0MotifTankyrase-binding domain
HgeneNUMA1chr11:71746948chr9:39074008ENST00000358965-4271984_1989142102.0MotifNuclear localization signal
HgeneNUMA1chr11:71746948chr9:39074008ENST00000393695-3271742_1748142116.0MotifTankyrase-binding domain
HgeneNUMA1chr11:71746948chr9:39074008ENST00000393695-3271984_1989142116.0MotifNuclear localization signal
HgeneNUMA1chr11:71746948chr9:39074008ENST00000358965-4271699_1876142102.0RegionMembrane-binding domain 1
HgeneNUMA1chr11:71746948chr9:39074008ENST00000358965-4271700_2115142102.0RegionNote=Tail (Globular)
HgeneNUMA1chr11:71746948chr9:39074008ENST00000358965-4271788_1810142102.0Region4.1-binding domain
HgeneNUMA1chr11:71746948chr9:39074008ENST00000358965-4271882_1985142102.0RegionTubulin-binding domain
HgeneNUMA1chr11:71746948chr9:39074008ENST00000358965-4271892_1926142102.0RegionGPSM2-binding domain
HgeneNUMA1chr11:71746948chr9:39074008ENST00000358965-4271981_2060142102.0RegionMembrane-binding domain 2
HgeneNUMA1chr11:71746948chr9:39074008ENST00000358965-4271_212142102.0RegionNote=Head (Globular)
HgeneNUMA1chr11:71746948chr9:39074008ENST00000393695-3271699_1876142116.0RegionMembrane-binding domain 1
HgeneNUMA1chr11:71746948chr9:39074008ENST00000393695-3271700_2115142116.0RegionNote=Tail (Globular)
HgeneNUMA1chr11:71746948chr9:39074008ENST00000393695-3271788_1810142116.0Region4.1-binding domain
HgeneNUMA1chr11:71746948chr9:39074008ENST00000393695-3271882_1985142116.0RegionTubulin-binding domain
HgeneNUMA1chr11:71746948chr9:39074008ENST00000393695-3271892_1926142116.0RegionGPSM2-binding domain
HgeneNUMA1chr11:71746948chr9:39074008ENST00000393695-3271981_2060142116.0RegionMembrane-binding domain 2
HgeneNUMA1chr11:71746948chr9:39074008ENST00000393695-3271_212142116.0RegionNote=Head (Globular)
TgeneCNTNAP3chr11:71746948chr9:39074008ENST00000297668222442_4812481289.0Compositional biasNote=Poly-Ser
TgeneCNTNAP3chr11:71746948chr9:39074008ENST0000029766822241015_120312481289.0DomainLaminin G-like 4
TgeneCNTNAP3chr11:71746948chr9:39074008ENST000002976682224183_36412481289.0DomainLaminin G-like 1
TgeneCNTNAP3chr11:71746948chr9:39074008ENST000002976682224370_54512481289.0DomainLaminin G-like 2
TgeneCNTNAP3chr11:71746948chr9:39074008ENST000002976682224551_58312481289.0DomainEGF-like 1
TgeneCNTNAP3chr11:71746948chr9:39074008ENST000002976682224584_79212481289.0DomainFibrinogen C-terminal
TgeneCNTNAP3chr11:71746948chr9:39074008ENST000002976682224793_95812481289.0DomainLaminin G-like 3
TgeneCNTNAP3chr11:71746948chr9:39074008ENST000002976682224962_99612481289.0DomainEGF-like 2
TgeneCNTNAP3chr11:71746948chr9:39074008ENST00000297668222426_124512481289.0Topological domainExtracellular


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Fusion Gene Sequence for NUMA1-CNTNAP3


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.
>60898_60898_1_NUMA1-CNTNAP3_NUMA1_chr11_71746948_ENST00000358965_CNTNAP3_chr9_39074008_ENST00000297668_length(transcript)=1545nt_BP=300nt
GCCCACGAAGAGGTACGATTCCGGAGAATCGCGAGGCAGAGCGGGAGCGCGCAGCCAGGTGGAAACTAATTCTAAGCCAGACTGCTGGAG
ATCACCCTGTTCTAGTGTGTGGAGGCTTCCACCAGGAGTCTGGAGTGCAATGGCACGATCTCGGCTCACTGCAACCTCCACCTCCCAGGT
TCAAGCGATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGATTACAGGCGCATTGGAGTGACTGTCTGGCATCACCAAGATGACACTCCAC
GCCACCCGGGGGGCTGCACTCCTCTCTTGGGTGTGATAGCAGTGGTGATATTTATTTTGCTTTGCATCACTGCCATAGCCATACGCATCT
ATCAACAGAGAAAGTTACGCAAAGAAAATGAGTCAAAAGTCTCAAAAAAAGAAGAGTGCTAGGACAGCTCTAAACAGTGAGCTCGATGTG
CAAAACGCAGTCCATGAAAACCAGAAAGAGCGAGTCTTCTGATTGGCAGCTGTGGCTGTCTCTATCATCGTGACTGTGGACTTCCCTGCT
GTTGCCATCAGGGTGCACACAAGCAGGTGCAGTGCTGTCACCTGGCTGAAGACCTGCAGCCTCGGAGCCTCTGGGAGGTCCCTTTCTCCC
TCGGTGAAACACAGTCCTCCACATCAATTTCCAAACAATGAATTAGGTATGGCCATTCATCACTGTTCAGTAGTTTCCCCGTCCAAAGGC
TCTCTTCCAAAACTGCAGTTTGATCTGTGTTAATAATTGTGGGGTTTTAGATGAGAAAATGGCTATAAAGCTGTGGCCCTACTTTATTTT
TTAAAAATGACAGAACTTTTGTTCAGATGTAAAAGACAAAATTGCACTTTAATGTTTTTTGTTACTTGAAAACATATCTGGGATCCCTTT
TTTTGGTCCTCTGCTGATATTTATAAAACAAGAAATGCTTCTTGGACTACCTTCACTGGCATTTCCATAGTCCTGGAATCCAGAGCCAAG
TGGCCTATCTAAAATTCACAGCCCTTTTATTCTCCTGTGTGATGGTTAATACAACACAGTTGAAGCCTGGAAACACTACCATTATTTTTG
GTGTATTGCTTTTTCTAATTGACTGTTTTTAATGATTTTGATACATTTTAATGTTGAAATTAATATTGAATGTTAGCTATGAAATTTTAG
TATTGAATTTTATAATGGAACAGAACATTGGTAGGTAACAAGATGCAAGAGGATGTCAATACAAGATTGTCTGCCTGTTTTTCTTTGTAA
TTTGTAATTACAGTTTTTGTAACTTGTGATTATGTTTTTAACTAAATTTACCACCAGATACAAACAATACTTCTTACACAGAGTTATCCT
TTATTTATATCATTAAGACGTGAATGAAACATCATCCTAACTTACTTCCCCAAGATATTGAGAGGTCATATCTGTTTTTCTTTATCATTC
ATTTCTTTTTCTAAAAGTTGTTACTGATATGCTTTTGATTTCCTATGACTCTATTATGTTGTACAGAACATCTTTTCAATTTATTAAAAA

>60898_60898_1_NUMA1-CNTNAP3_NUMA1_chr11_71746948_ENST00000358965_CNTNAP3_chr9_39074008_ENST00000297668_length(amino acids)=87AA_BP=46

--------------------------------------------------------------

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Fusion Gene PPI Analysis for NUMA1-CNTNAP3


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 NUMA1-CNTNAP3


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 NUMA1-CNTNAP3


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