CYLD
protein-codingCYLD lysine 63 deubiquitinase, the group of Ubiquitin specific peptidases|MicroRNA protein coding host genes
Gene summary
This gene is encodes a cytoplasmic protein with three cytoskeletal-associated protein-glycine-conserved (CAP-GLY) domains that functions as a deubiquitinating enzyme. Mutations in this gene have been associated with cylindromatosis, multiple familial trichoepithelioma, and Brooke-Spiegler syndrome. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
- CYLD1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~59.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0042977
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0004976
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0011512
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0011512
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0011114
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0007565
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0030872
Submitter: ClinGen
*CYLD* was first considered a causal gene for autosomal dominant frontotemporal dementia (FTD) and/or amyotrophic lateral sclerosis type 8 (ALS8) in 2020 following whole genome sequencing of two affected members and one unaffected member of a large family of European Australian decent. (Dobson-Stone et al., PMID: 32185393). *CYLD* codes for a deubiquitinating enzyme that specifically cleaves ‘Lys-63’-and linear ‘Met-1’ linked polyubiquitin chains and is involved in regulating NF-κB activation, Wnt signaling and TNF-alpha-induced necroptosis. *CYLD* has also been reported to cause a group of inherited skin adnexal tumor syndromes called *CYLD* cutaneous syndromes. Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found difference in molecular mechanism and phenotypic variability. Therefore, the following disease entities have been split into multiple disease entities, autosomal dominant FTD and/or ALS8 (OMIM:619132) and autosomal dominant CYLD Cutaneous Syndromes: Brooke-Spiegler Syndrome (OMIM:605041), familial cylindromatosis (OMIM:132700), and multiple familial trichoepithelioma (OMIM:601606). The split curation for autosomal dominant Brooke-Spiegler Syndrome has been curated separately. Five missense variants that have been reported in five probands in two publications (PMIDs: 32185393 and 3468212) are included in this curation. Other missense variants reported in the literature have been excluded from scoring due to being outside the expert panel’s MAF cutoff (>0.00001) or not having an ALS phenotype (PMIDs: 36000313, 3468212, and 32666117). The mechanism of pathogenicity appears to be gain of function. This gene-disease association is also supported by experimental evidence; the preponderance coming from assays expressing the variant Met719Val (PMID: 32185393). Neuropathologic analysis of postmortem brain tissue of 2 affected individuals showed widespread glial *CYLD* immunoreactivity that was not present in other patients with sporadic FTD. There were also patchy areas of diffuse neuronal cytoplasmic *CYLD* staining in the hippocampus and frontal cortex, as well as *CYLD* immunoreactivity in the nuclei of pyknotic neurons. Transfection of primary mouse cortical neurons with mutant M719V *CYLD* resulted in an increased proportion of neurons with cytoplasmic TDP-43 staining (~55%) compared to cells transfected with wildtype *CYLD* (~34%). Co-transfection of flagged *CYLD* constructs followed by immunoprecipitation with anti-FLAG antibody reveals *CYLD* interacts with known ALS genes *OPTN*, *TBK1* and *SQSTM1*, though M719V does not abrogate the interaction. Additional in vitro cellular studies show that the M719V mutation resulted in impaired autophagosome fusion with lysosomes compared to wildtype. In summary, there is limited evidence to support this gene-disease relationship. Although more evidence is needed to support a causal role, no convincing evidence has emerged that contradicts the gene-disease relationship. This classification was approved by the ClinGen ALS GCEP on February 23, 2023 (SOP Version 9).
Inheritance Pattern: AD
Disease ID:MONDO:0030872
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0011512
Submitter: ClinGen
There is abundant evidence published associating the CYLD gene with Brooke-Spiegler syndrome, since the gene-disease relationship was first proposed by Bignell et al. (2000). Multiple case level studies have been performed with BSS patients that have variants in the CYLD gene. CYLD protein is prominently expressed in the inner root sheath of hair follicles of human scalp as well as in eccrine glands. Multiple articles reported no CYLD protein expression in the tumour tissue from BSS patients. Loss of CYLD inhibits apoptosis by activating NF-kappaB. Cyld also negatively regulate cell proliferation in keratinocytes and human Cylindroma tumors display hyperactive Wnt signaling. Cyld-/- mice are highly sensitive to skin tumor development under TPA or UV-B treatment. All of these types of evidence are consistent with a definitive relationship between the CYLD gene and Brooke-Spiegler syndrome.
Inheritance Pattern: AD
Disease ID:MONDO:0007565
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0007565
Submitter: Orphanet
Clinical Genomic Database (CGD)
Manifestation: Dermatologic; Neurologic; Oncologic
Intervention: Dermatologic; Oncologic
Rationale: The conditions can include a number of types of cancerous lesions for which surveillance/treatment (including surgical management) may be beneficial; In familial trichoepithelioma, skin lesions can degenerate into basal cell carcinoma; In Cylindromatosis, familial, childhood tumors have been reported, and neoplasms may undergo malignant transformation; Individuals are at risk of salivary/parotid adenocarcinoma
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CYLD variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001378743.1. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 7 | 54 | 1 | 62 | ||
| missense | 3 | 2 | 164 | 8 | 3 | 180 |
| nonsense | 22 | 10 | 32 | |||
| start loss | 0 | |||||
| frameshift | 34 | 13 | 47 | |||
| splice donor/acceptor (+/-2bp) | 8 | 4 | 6 | 18 | ||
| Total | 67 | 29 | 177 | 62 | 4 | 339 |
Highest pathogenic variant AF is 0.000004439748
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001365672.1 | 17 | MANE Select | |
| Ensembl | ENSP00000392025.3 | 17 | MANE Select | |
| RefSeq | NP_001035814.1 | 16 | Standard | |
| RefSeq | NP_001035877.1 | 16 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| cyldb | Danio rerio | Structure: pharyngeal arch cartilage Quality: malformed abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Necroptosis - Homo sapiens (human)
- C-type lectin receptor signaling pathway - Homo sapiens (human)
- Osteoclast differentiation - Homo sapiens (human)
- RIG-I-like receptor signaling pathway - Homo sapiens (human)
- Regulation of toll-like receptor signaling pathway
Biological Process
- ubiquitin-dependent protein catabolic process
- cell cycle
- regulation of mitotic cell cycle
- regulation of tumor necrosis factor-mediated signaling pathway
- Wnt signaling pathway
Molecular Function
- thiol-dependent ubiquitin-specific protease activity
- protein binding
- zinc ion binding
- protein kinase binding
- thiol-dependent ubiquitinyl hydrolase activity
Cellular Component
- centrosome
- spindle
- cytosol
- cytoplasmic microtubule
- midbody
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000427738
- Coding exons
- 17
- Length
- 59886
- Individuals with no LoFs
- 124788
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 7
- Defined
- 124795
- p
- 0.0000280
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.55 | 277 | 500 | 0.554 | 0.0000255 | 6275 |
| Missense (PolyPhen) | 79 | 180.53 | 0.43761 | 2315 | ||
| Synonymous | 0.323 | 178 | 184 | 0.970 | 0.0000102 | 1795 |
| Loss of Function | 5.65 | 4 | 44.8 | 0.0893 | 0.00000207 | 616 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000053 | 0.000053 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- 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}.;
- Disease
- DISEASE: Cylindromatosis, familial (FCYL) [MIM:132700]: A disorder characterized by multiple skin tumors that develop from skin appendages, such as hair follicles and sweat glands. Affected individuals typically develop large numbers of tumors called cylindromas that arise predominantly in hairy parts of the body with approximately 90% on the head and neck. In severely affected individuals, cylindromas may combine into a confluent mass which may ulcerate or become infected (turban tumor syndrome). Individuals with familial cylindromatosis occasionally develop other types of tumors including spiradenomas that begin in sweat glands, and trichoepitheliomas arising from hair follicles. {ECO:0000269|PubMed:12190880, ECO:0000269|PubMed:16922728}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Multiple familial trichoepithelioma 1 (MFT1) [MIM:601606]: Autosomal dominant dermatosis characterized by the presence of many skin tumors predominantly on the face. Since histologic examination shows dermal aggregates of basaloid cells with connection to or differentiation toward hair follicles, this disorder has been thought to represent a benign hamartoma of the pilosebaceous apparatus. Trichoepitheliomas can degenerate into basal cell carcinoma. {ECO:0000269|PubMed:14632188, ECO:0000269|PubMed:16307661, ECO:0000269|PubMed:16922728}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Brooke-Spiegler syndrome (BRSS) [MIM:605041]: An autosomal dominant disorder characterized by the appearance of multiple skin appendage tumors such as cylindroma, trichoepithelioma, and spiradenoma. These tumors are typically located in the head and neck region, appear in early adulthood, and gradually increase in size and number throughout life. {ECO:0000269|PubMed:12190880, ECO:0000269|PubMed:12950348, ECO:0000269|PubMed:14632188, ECO:0000269|PubMed:15854031}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.309
Intolerance Scores
- LoFtool
- 0.0672
- RVIS EVS
- -0.93
- RVIS percentile EVS
- 9.47
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- K
- Indispensability pred.
- E
- Indispensability score
- 0.916
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |