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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:CYLD-FAM49B (FusionGDB2 ID:20991)

Fusion Gene Summary for CYLD-FAM49B

check button Fusion gene summary
Fusion gene informationFusion gene name: CYLD-FAM49B
Fusion gene ID: 20991
HgeneTgene
Gene symbol

CYLD

FAM49B

Gene ID

1540

51571

Gene nameCYLD lysine 63 deubiquitinaseCYFIP related Rac1 interactor B
SynonymsBRSS|CDMT|CYLD1|CYLDI|EAC|MFT|MFT1|SBS|TEM|USPL2BM-009|CYRI|CYRI-B|FAM49B|L1
Cytomap

16q12.1

8q24.21

Type of geneprotein-codingprotein-coding
Descriptionubiquitin carboxyl-terminal hydrolase CYLDcylindromatosis (turban tumor syndrome)deubiquitinating enzyme CYLDprobable ubiquitin carboxyl-terminal hydrolase CYLDubiquitin specific peptidase like 2ubiquitin thioesterase CYLDubiquitin thiolesterase CYLprotein FAM49BFAM49B/JPH1 fusionMTSS1/FAM49B fusionfamily with sequence similarity 49 member B
Modification date2020032920200313
UniProtAcc

Q9NQC7

.
Ensembl transtripts involved in fusion geneENST00000311559, ENST00000398568, 
ENST00000427738, ENST00000540145, 
ENST00000569418, ENST00000564326, 
ENST00000566206, ENST00000568704, 
ENST00000401979, ENST00000517654, 
ENST00000518879, ENST00000519110, 
ENST00000523509, ENST00000519540, 
ENST00000519824, ENST00000522250, 
ENST00000522746, ENST00000522941, 
Fusion gene scores* DoF score6 X 4 X 4=9616 X 17 X 9=2448
# samples 620
** MAII scorelog2(6/96*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(20/2448*10)=-3.61353165291793
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CYLD [Title/Abstract] AND FAM49B [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCYLD(50776752)-FAM49B(130983241), # samples:3
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
HgeneCYLD

GO:0010803

regulation of tumor necrosis factor-mediated signaling pathway

26997266|27458237|27591049

HgeneCYLD

GO:0016579

protein deubiquitination

29291351

HgeneCYLD

GO:0032088

negative regulation of NF-kappaB transcription factor activity

18313383

HgeneCYLD

GO:0045087

innate immune response

26997266

HgeneCYLD

GO:0046329

negative regulation of JNK cascade

29291351

HgeneCYLD

GO:0050727

regulation of inflammatory response

27591049

HgeneCYLD

GO:0060544

regulation of necroptotic process

27458237

HgeneCYLD

GO:0070536

protein K63-linked deubiquitination

18313383|18636086|26997266|27458237|27591049|29291351

HgeneCYLD

GO:1901223

negative regulation of NIK/NF-kappaB signaling

18313383

HgeneCYLD

GO:1903753

negative regulation of p38MAPK cascade

29291351

HgeneCYLD

GO:1990108

protein linear deubiquitination

26997266|27458237|27591049


check buttonFusion gene breakpoints across CYLD (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 FAM49B (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
ChimerDB4PRADTCGA-VP-A87D-01ACYLDchr16

50776752

-FAM49Bchr8

130983241

-
ChimerDB4PRADTCGA-VP-A87D-01ACYLDchr16

50776752

+FAM49Bchr8

130983241

-
ChimerDB4PRADTCGA-VP-A87DCYLDchr16

50776752

+FAM49Bchr8

130983241

-


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Fusion Gene ORF analysis for CYLD-FAM49B

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
5UTR-5UTRENST00000311559ENST00000401979CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-5UTRENST00000311559ENST00000517654CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-5UTRENST00000311559ENST00000518879CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-5UTRENST00000311559ENST00000519110CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-5UTRENST00000311559ENST00000523509CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-5UTRENST00000398568ENST00000401979CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-5UTRENST00000398568ENST00000517654CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-5UTRENST00000398568ENST00000518879CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-5UTRENST00000398568ENST00000519110CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-5UTRENST00000398568ENST00000523509CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-5UTRENST00000427738ENST00000401979CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-5UTRENST00000427738ENST00000517654CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-5UTRENST00000427738ENST00000518879CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-5UTRENST00000427738ENST00000519110CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-5UTRENST00000427738ENST00000523509CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-5UTRENST00000540145ENST00000401979CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-5UTRENST00000540145ENST00000517654CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-5UTRENST00000540145ENST00000518879CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-5UTRENST00000540145ENST00000519110CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-5UTRENST00000540145ENST00000523509CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-5UTRENST00000569418ENST00000401979CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-5UTRENST00000569418ENST00000517654CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-5UTRENST00000569418ENST00000518879CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-5UTRENST00000569418ENST00000519110CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-5UTRENST00000569418ENST00000523509CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-intronENST00000311559ENST00000519540CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-intronENST00000311559ENST00000519824CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-intronENST00000311559ENST00000522250CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-intronENST00000311559ENST00000522746CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-intronENST00000311559ENST00000522941CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-intronENST00000398568ENST00000519540CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-intronENST00000398568ENST00000519824CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-intronENST00000398568ENST00000522250CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-intronENST00000398568ENST00000522746CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-intronENST00000398568ENST00000522941CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-intronENST00000427738ENST00000519540CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-intronENST00000427738ENST00000519824CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-intronENST00000427738ENST00000522250CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-intronENST00000427738ENST00000522746CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-intronENST00000427738ENST00000522941CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-intronENST00000540145ENST00000519540CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-intronENST00000540145ENST00000519824CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-intronENST00000540145ENST00000522250CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-intronENST00000540145ENST00000522746CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-intronENST00000540145ENST00000522941CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-intronENST00000569418ENST00000519540CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-intronENST00000569418ENST00000519824CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-intronENST00000569418ENST00000522250CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-intronENST00000569418ENST00000522746CYLDchr16

50776752

+FAM49Bchr8

130983241

-
5UTR-intronENST00000569418ENST00000522941CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-5UTRENST00000564326ENST00000401979CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-5UTRENST00000564326ENST00000517654CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-5UTRENST00000564326ENST00000518879CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-5UTRENST00000564326ENST00000519110CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-5UTRENST00000564326ENST00000523509CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-5UTRENST00000566206ENST00000401979CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-5UTRENST00000566206ENST00000517654CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-5UTRENST00000566206ENST00000518879CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-5UTRENST00000566206ENST00000519110CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-5UTRENST00000566206ENST00000523509CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-5UTRENST00000568704ENST00000401979CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-5UTRENST00000568704ENST00000517654CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-5UTRENST00000568704ENST00000518879CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-5UTRENST00000568704ENST00000519110CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-5UTRENST00000568704ENST00000523509CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-intronENST00000564326ENST00000519540CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-intronENST00000564326ENST00000519824CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-intronENST00000564326ENST00000522250CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-intronENST00000564326ENST00000522746CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-intronENST00000564326ENST00000522941CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-intronENST00000566206ENST00000519540CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-intronENST00000566206ENST00000519824CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-intronENST00000566206ENST00000522250CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-intronENST00000566206ENST00000522746CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-intronENST00000566206ENST00000522941CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-intronENST00000568704ENST00000519540CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-intronENST00000568704ENST00000519824CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-intronENST00000568704ENST00000522250CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-intronENST00000568704ENST00000522746CYLDchr16

50776752

+FAM49Bchr8

130983241

-
intron-intronENST00000568704ENST00000522941CYLDchr16

50776752

+FAM49Bchr8

130983241

-

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 CYLD-FAM49B


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 CYLD-FAM49B


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/:50776752/:130983241)
- 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
CYLD

Q9NQC7

.
FUNCTION: Deubiquitinase that specifically cleaves 'Lys-63'- and linear 'Met-1'-linked polyubiquitin chains and is involved in NF-kappa-B activation and TNF-alpha-induced necroptosis (PubMed:18636086, PubMed:26670046, PubMed:27458237, PubMed:26997266, PubMed:27591049, PubMed:29291351, PubMed:18313383). Plays an important role in the regulation of pathways leading to NF-kappa-B activation (PubMed:12917689, PubMed:12917691). Contributes to the regulation of cell survival, proliferation and differentiation via its effects on NF-kappa-B activation (PubMed:12917690). Negative regulator of Wnt signaling (PubMed:20227366). Inhibits HDAC6 and thereby promotes acetylation of alpha-tubulin and stabilization of microtubules (PubMed:19893491). Plays a role in the regulation of microtubule dynamics, and thereby contributes to the regulation of cell proliferation, cell polarization, cell migration, and angiogenesis (PubMed:18222923, PubMed:20194890). Required for normal cell cycle progress and normal cytokinesis (PubMed:17495026, PubMed:19893491). Inhibits nuclear translocation of NF-kappa-B (PubMed:18636086). Plays a role in the regulation of inflammation and the innate immune response, via its effects on NF-kappa-B activation (PubMed:18636086). Dispensable for the maturation of intrathymic natural killer cells, but required for the continued survival of immature natural killer cells (By similarity). Negatively regulates TNFRSF11A signaling and osteoclastogenesis (By similarity). Involved in the regulation of ciliogenesis, allowing ciliary basal bodies to migrate and dock to the plasma membrane; this process does not depend on NF-kappa-B activation (By similarity). Ability to remove linear ('Met-1'-linked) polyubiquitin chains regulates innate immunity and TNF-alpha-induced necroptosis: recruited to the LUBAC complex via interaction with SPATA2 and restricts linear polyubiquitin formation on target proteins (PubMed:26997266, PubMed:26670046, PubMed:27458237, PubMed:27591049). Regulates innate immunity by restricting linear polyubiquitin formation on RIPK2 in response to NOD2 stimulation (PubMed:26997266). Involved in TNF-alpha-induced necroptosis by removing linear ('Met-1'-linked) polyubiquitin chains from RIPK1, thereby regulating the kinase activity of RIPK1 (By similarity). Removes 'Lys-63' linked polyubiquitin chain of MAP3K7, which inhibits phosphorylation and blocks downstream activation of the JNK-p38 kinase cascades (PubMed:29291351). {ECO:0000250|UniProtKB:Q80TQ2, ECO:0000269|PubMed:12917689, ECO:0000269|PubMed:12917690, ECO:0000269|PubMed:12917691, ECO:0000269|PubMed:17495026, ECO:0000269|PubMed:18222923, ECO:0000269|PubMed:18313383, ECO:0000269|PubMed:18636086, ECO:0000269|PubMed:19893491, ECO:0000269|PubMed:20194890, ECO:0000269|PubMed:20227366, ECO:0000269|PubMed:26670046, ECO:0000269|PubMed:26997266, ECO:0000269|PubMed:27458237, ECO:0000269|PubMed:27591049, ECO:0000269|PubMed:29291351}.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 CYLD-FAM49B


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 CYLD-FAM49B


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 CYLD-FAM49B


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 CYLD-FAM49B


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