CDSN

protein-coding

corneodesmosin

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

NM_001264.5

Inheritance

AR, AD

ClinVar variants

P:9U:79B:47

Top phenotype

Hypotrichosis 2; Peeling skin syndrome 1

gnomAD constraint

pLI —, LoF o/e 0.2

Max pathogenic AF

—

Genomic locus

chr6:31,115,087-31,120,446

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~5.4 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

peeling skin syndrome 1STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0024548

Submitter: Genomics England PanelApp

hypotrichosis 2MODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0007805

Submitter: Ambry Genetics

hypotrichosis 2STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007805

Submitter: Labcorp Genetics (formerly Invitae)

hypotrichosis simplex of the scalpSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0019575

Submitter: Orphanet

hypotrichosis 2LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0007805

Submitter: G2P

peeling skin syndrome 1MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0024548

Submitter: Ambry Genetics

peeling skin syndrome 1STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0024548

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Hypotrichosis 2; Peeling skin syndrome 1AD/AR

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

Refs: 3652491; 10793007; 12754508; 20691404; 21191406; 21777220; 22146835Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CDSN variants in ClinVar

7 Conditions Cataloged
not providedTotal: 77
Inborn genetic diseasesTotal: 52
CDSN-related disorderTotal: 21
not specifiedTotal: 16
Peeling skin syndrome 1Total: 10
Hypotrichosis 2Total: 5
Serum phosphorus normal or mildly elevatedTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
23
clinvar
3
clinvar
27
missense
1
clinvar
74
clinvar
14
clinvar
7
clinvar
96
nonsense
4
clinvar
1
clinvar
5
start loss
0
frameshift
1
clinvar
2
clinvar
4
clinvar
7
splice donor/acceptor (+/-2bp)
0
Total54793710135

Highest pathogenic variant AF is 0.00004233874

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001264.5RefSeqNP_001255.42MANE Select
ENST00000376288.3EnsemblENSP00000365465.22MANE 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.012472960.8340.00001643361
Missense (PolyPhen)2322.9911.0004199
Synonymous0.8621131250.9020.000007931143
Loss of Function2.35210.00.2004.95e-7115

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish0.000100.000099rare
East Asian0.0000540.000054rare
Finnish00.0absent
European (Non-Finnish)0.0000470.000035rare
South Asian0.0000980.000098rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.