CDSN
protein-codingcorneodesmosin
Gene summary
This gene encodes a protein found in corneodesmosomes, which localize to human epidermis and other cornified squamous epithelia. The encoded protein undergoes a series of cleavages during corneocyte maturation. This gene is highly polymorphic in human populations, and variation has been associated with skin diseases such as psoriasis, hypotrichosis and peeling skin syndrome. The gene is located in the major histocompatibility complex (MHC) class I region on chromosome 6. [provided by RefSeq, Dec 2014]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~5.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0024548
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0007805
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0007805
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0019575
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0007805
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0024548
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0024548
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Allergy/Immunology/Infectious; Dermatologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CDSN variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001264.5. 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 | 1 | 23 | 3 | 27 | ||
| missense | 1 | 74 | 14 | 7 | 96 | |
| nonsense | 4 | 1 | 5 | |||
| start loss | 0 | |||||
| frameshift | 1 | 2 | 4 | 7 | ||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 5 | 4 | 79 | 37 | 10 | 135 |
Highest pathogenic variant AF is 0.00004233874
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001255.4 | 2 | MANE Select | |
| Ensembl | ENSP00000365465.2 | 2 | MANE Select |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Keratinization
- Developmental Biology
- Formation of the cornified envelope
Biological Process
- corneocyte desquamation
- cell adhesion
- epidermis development
- keratinocyte differentiation
- skin morphogenesis
Molecular Function
- protein homodimerization activity
Cellular Component
- cornified envelope
- extracellular region
- plasma membrane
- cell-cell junction
- desmosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000376288
- Coding exons
- 2
- Length
- 5357
- Individuals with no LoFs
- 125737
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 9
- Defined
- 125746
- p
- 0.0000358
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.01 | 247 | 296 | 0.834 | 0.0000164 | 3361 |
| Missense (PolyPhen) | 23 | 22.991 | 1.0004 | 199 | ||
| Synonymous | 0.862 | 113 | 125 | 0.902 | 0.00000793 | 1143 |
| Loss of Function | 2.35 | 2 | 10.0 | 0.200 | 4.95e-7 | 115 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000047 | 0.000035 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Important for the epidermal barrier integrity. {ECO:0000269|PubMed:20691404}.;
- Disease
- DISEASE: Hypotrichosis 2 (HYPT2) [MIM:146520]: A condition characterized by the presence of less than the normal amount of hair. Affected individuals have normal hair in early childhood but experience progressive hair loss limited to the scalp beginning in the middle of the first decade and almost complete baldness by the third decade. Body hair, beard, eyebrows, axillary hair, teeth, and nails develop normally. {ECO:0000269|PubMed:12754508}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Peeling skin syndrome 1 (PSS1) [MIM:270300]: A genodermatosis characterized by generalized, continuous shedding of the outer layers of the epidermis. Two main PSS subtypes have been suggested. Patients with non-inflammatory PSS (type A) manifest white scaling, with painless and easy removal of the skin, irritation when in contact with water, dust and sand, and no history of erythema, pruritis or atopy. Inflammatory PSS (type B) is associated with generalized erythema, pruritus and atopy. It is an ichthyosiform erythroderma characterized by lifelong patchy peeling of the entire skin with onset at birth or shortly after. Several patients have been reported with high IgE levels. {ECO:0000269|PubMed:20691404}. Note=The disease is caused by mutations affecting the gene represented in this entry. CDNS mutations are responsible for generalized, inflammatory peeling skin syndrome type B (PubMed:20691404). {ECO:0000269|PubMed:20691404}.;
Intolerance Scores
- LoFtool
- 0.599
- RVIS EVS
- 2.11
- RVIS percentile EVS
- 97.89
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.522
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | High | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |