KRT10
protein-codingkeratin 10, the group of Keratins, type I
Gene summary
This gene encodes a member of the type I (acidic) cytokeratin family, which belongs to the superfamily of intermediate filament (IF) proteins. Keratins are heteropolymeric structural proteins which form the intermediate filament. These filaments, along with actin microfilaments and microtubules, compose the cytoskeleton of epithelial cells. Mutations in this gene are associated with epidermolytic hyperkeratosis. This gene is located within a cluster of keratin family members on chromosome 17q21. [provided by RefSeq, Jul 2008]
- KPP
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~4.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0019269
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0100303
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0700245
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0007239
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0700248
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0007239
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0044742
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0700248
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0012208
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0700245
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0011870
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0011870
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0007239
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0011870
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0012208
Submitter: Orphanet
Clinical Genomic Database (CGD)
Manifestation: 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 KRT10 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000421.5. 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 | 47 | 4 | 52 | ||
| missense | 16 | 14 | 96 | 15 | 7 | 148 |
| nonsense | 2 | 2 | 1 | 5 | ||
| start loss | 0 | |||||
| frameshift | 4 | 1 | 4 | 1 | 10 | |
| splice donor/acceptor (+/-2bp) | 6 | 2 | 1 | 9 | ||
| Total | 28 | 19 | 103 | 62 | 12 | 224 |
Highest pathogenic variant AF is 0.00000656918
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000412.4 | 8 | MANE Select | |
| Ensembl | ENSP00000269576.5 | 8 | MANE Select | |
| RefSeq | NP_001366295.1 | 8 | Standard | |
| Ensembl | ENSP00000490524.2 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Staphylococcus aureus infection - Homo sapiens (human)
- Estrogen signaling pathway - Homo sapiens (human)
- Hair Follicle Development- Induction (Part 1 of 3)
- Keratinization
- Developmental Biology
Biological Process
- peptide cross-linking
- keratinocyte differentiation
- keratinization
- positive regulation of epidermis development
- protein heterotetramerization
Molecular Function
- structural constituent of epidermis
- protein heterodimerization activity
Cellular Component
- cornified envelope
- extracellular space
- nucleus
- cytoplasm
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000269576
- Coding exons
- 8
- Length
- 4479
- Individuals with no LoFs
- 125732
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 16
- Defined
- 125748
- p
- 0.0000636
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.253 | 280 | 292 | 0.958 | 0.0000160 | 3704 |
| Missense (PolyPhen) | 94 | 118.62 | 0.79242 | 1548 | ||
| Synonymous | -1.56 | 141 | 119 | 1.18 | 0.00000619 | 1210 |
| Loss of Function | 3.00 | 9 | 25.3 | 0.356 | 0.00000132 | 304 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000044 | 0.000044 | rare |
| South Asian | 0.00026 | 0.00020 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays a role in the establishment of the epidermal barrier on plantar skin. {ECO:0000250|UniProtKB:P02535}.;
- Disease
- DISEASE: Epidermolytic hyperkeratosis (EHK) [MIM:113800]: An autosomal dominant skin disorder characterized by widespread blistering and an ichthyotic erythroderma at birth that persist into adulthood. Histologically there is a diffuse epidermolytic degeneration in the lower spinous layer of the epidermis. Within a few weeks from birth, erythroderma and blister formation diminish and hyperkeratoses develop. {ECO:0000269|PubMed:10201536, ECO:0000269|PubMed:1380725, ECO:0000269|PubMed:1381287, ECO:0000269|PubMed:21271994, ECO:0000269|PubMed:7507150, ECO:0000269|PubMed:7507152, ECO:0000269|PubMed:7508181, ECO:0000269|PubMed:7512983, ECO:0000269|PubMed:7526210, ECO:0000269|Ref.7}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Ichthyosis annular epidermolytic (AEI) [MIM:607602]: A skin disorder resembling bullous congenital ichthyosiform erythroderma. Affected individuals present with bullous ichthyosis in early childhood and hyperkeratotic lichenified plaques in the flexural areas and extensor surfaces at later ages. The feature that distinguishes AEI from BCIE is dramatic episodes of flares of annular polycyclic plaques with scale, which coalesce to involve most of the body surface and can persist for several weeks or even months. {ECO:0000269|PubMed:9036939, ECO:0000269|PubMed:9856845}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Erythroderma, ichthyosiform, congenital reticular (CRIE) [MIM:609165]: A rare skin condition characterized by slowly enlarging islands of normal skin surrounded by erythematous ichthyotic patches in a reticulated pattern. The condition starts in infancy as a lamellar ichthyosis, with small islands of normal skin resembling confetti appearing in late childhood and at puberty. Histopathologic findings include band-like parakeratosis, psoriasiform acanthosis, and vacuolization of keratinocytes with binucleated cells in the upper epidermis, sometimes associated with amyloid deposition in the dermis. Ultrastructural abnormalities include perinuclear shells formed from a network of fine filaments in the upper epidermis. {ECO:0000269|PubMed:20798280}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.540
Intolerance Scores
- LoFtool
- 0.0859
- RVIS EVS
- 0.22
- RVIS percentile EVS
- 68.38
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.734
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |