KRT1
protein-codingkeratin 1, the group of Keratins, type II
Gene summary
The protein encoded by this gene is a member of the keratin gene family. The type II cytokeratins consist of basic or neutral proteins which are arranged in pairs of heterotypic keratin chains coexpressed during differentiation of simple and stratified epithelial tissues. This type II cytokeratin is specifically expressed in the spinous and granular layers of the epidermis with family member KRT10 and mutations in these genes have been associated with bullous congenital ichthyosiform erythroderma. The type II cytokeratins are clustered in a region of chromosome 12q12-q13. [provided by RefSeq, Jul 2008]
- EHK1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~5.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0007239
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0011870
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0010962
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0007808
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0011870
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0011870
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0007808
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0007239
Submitter: Illumina
Inheritance Pattern: AD
Disease ID:MONDO:0010962
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0012208
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0859574
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0018865
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0007239
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0007808
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0011218
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0100303
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0006590
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0019269
Submitter: PanelApp Australia
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 KRT1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006121.4. 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 | 4 | 31 | 4 | 39 | ||
| missense | 16 | 19 | 142 | 14 | 2 | 193 |
| nonsense | 1 | 2 | 3 | |||
| start loss | 1 | 1 | ||||
| frameshift | 8 | 2 | 6 | 16 | ||
| splice donor/acceptor (+/-2bp) | 7 | 2 | 1 | 10 | ||
| Total | 31 | 24 | 156 | 45 | 6 | 262 |
Highest pathogenic variant AF is 0.0000020521325
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006112.3 | 9 | MANE Select | |
| Ensembl | ENSP00000252244.3 | 9 | MANE Select |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Corticotropin-releasing hormone signaling pathway
- Keratinization
- Developmental Biology
- Neutrophil degranulation
- Innate Immune System
Biological Process
- complement activation, lectin pathway
- retina homeostasis
- response to oxidative stress
- peptide cross-linking
- keratinization
Molecular Function
- protein binding
- carbohydrate binding
- structural constituent of epidermis
- signaling receptor activity
- protein heterodimerization activity
Cellular Component
- cornified envelope
- extracellular region
- extracellular space
- nucleus
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000252244
- Coding exons
- 9
- Length
- 5672
- Individuals with no LoFs
- 125733
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 15
- Defined
- 125748
- p
- 0.0000596
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.252 | 349 | 363 | 0.963 | 0.0000222 | 4178 |
| Missense (PolyPhen) | 96 | 118.95 | 0.80708 | 1589 | ||
| Synonymous | 0.0494 | 142 | 143 | 0.995 | 0.00000929 | 1333 |
| Loss of Function | 3.85 | 5 | 26.3 | 0.190 | 0.00000156 | 288 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00014 | 0.00014 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000062 | 0.000062 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May regulate the activity of kinases such as PKC and SRC via binding to integrin beta-1 (ITB1) and the receptor of activated protein C kinase 1 (RACK1). In complex with C1QBP is a high affinity receptor for kininogen-1/HMWK. {ECO:0000269|PubMed:17956333, ECO:0000269|PubMed:21544310}.;
- 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:10232403, ECO:0000269|PubMed:10688370, ECO:0000269|PubMed:10844506, ECO:0000269|PubMed:11531804, ECO:0000269|PubMed:12406348, ECO:0000269|PubMed:1380725, ECO:0000269|PubMed:1381288, ECO:0000269|PubMed:21271994, ECO:0000269|PubMed:7507151, ECO:0000269|PubMed:7507152, ECO:0000269|PubMed:7512983, ECO:0000269|PubMed:9856846}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Ichthyosis hystrix, Curth-Macklin type (IHCM) [MIM:146590]: A genodermatosis with severe verrucous hyperkeratosis. Affected individuals manifest congenital verrucous black scale on the scalp, neck, and limbs with truncal erythema, palmoplantar keratoderma and keratoses on the lips, ears, nipples and buttocks. {ECO:0000269|PubMed:11286616}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Keratoderma, palmoplantar, non-epidermolytic (NEPPK) [MIM:600962]: A dermatological disorder characterized by well- demarcated hyperkeratosis is present over the palms and soles. A red band is frequently present at the periphery of the keratosis. It is usually non-transgredient, with a sharp demarcation of the lesions at the wrists. {ECO:0000269|PubMed:11286630, ECO:0000269|PubMed:7528239}. 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:10053007, ECO:0000269|PubMed:10597140}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Keratoderma, palmoplantar, striate 3 (SPPK3) [MIM:607654]: A dermatological disorder characterized by thickening of the stratum corneum and epidermal layers on palms and soles. There is no involvement of non-palmoplantar skin, and both hair and nails are normal. {ECO:0000269|PubMed:11982762}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.610
Intolerance Scores
- LoFtool
- 0.0564
- RVIS EVS
- 0.71
- RVIS percentile EVS
- 85.68
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.509
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | High | Medium | High |
| Cancer | High | High | High |