KRT1

protein-coding

keratin 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]

Previous symbols:
  • EHK1

MANE transcript

NM_006121.4

Inheritance

AD, AR

ClinVar variants

P:55U:156B:51

Top phenotype

Keratosis palmoplantaris striata III; Ichthyosis, cyclic, with epidermolytic hyperkeratosis; Ichthyosis, annular epidermolytic, 2; Ichthyosis histrix, Curth-Macklin type; Palmoplantar keratoderma, epidermolytic 2; Palmoplantar keratoderma, nonepidermolytic; Epidermolytic hyperkeratosis 1

gnomAD constraint

pLI —, LoF o/e 0.19

Max pathogenic AF

—

Genomic locus

chr12:52,674,736-52,680,407

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~5.7 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

epidermolytic ichthyosisSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007239

Submitter: Genomics England PanelApp

annular epidermolytic ichthyosisSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0011870

Submitter: Genomics England PanelApp

diffuse nonepidermolytic palmoplantar keratodermaSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0010962

Submitter: Orphanet

ichthyosis hystrix of Curth-MacklinSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007808

Submitter: Orphanet

annular epidermolytic ichthyosisSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0011870

Submitter: Orphanet

annular epidermolytic ichthyosisDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0011870

Submitter: G2P

ichthyosis hystrix of Curth-MacklinSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007808

Submitter: Genomics England PanelApp

epidermolytic ichthyosisMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0007239

Submitter: Illumina

diffuse nonepidermolytic palmoplantar keratodermaSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0010962

Submitter: Genomics England PanelApp

congenital reticular ichthyosiform erythrodermaSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0012208

Submitter: Orphanet

ichthyosis, annular epidermolytic, 2STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0859574

Submitter: Ambry Genetics

striate palmoplantar keratodermaSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0018865

Submitter: Orphanet

epidermolytic ichthyosisSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007239

Submitter: Orphanet

ichthyosis hystrix of Curth-MacklinDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007808

Submitter: G2P

autosomal recessive congenital ichthyosis 11LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0011218

Submitter: Ambry Genetics

ichthyosis, annular epidermolytic 1STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0100303

Submitter: Labcorp Genetics (formerly Invitae)

palmoplantar keratosisSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0006590

Submitter: PanelApp Australia

ichthyosisSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0019269

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Keratosis palmoplantaris striata III; Ichthyosis, cyclic, with epidermolytic hyperkeratosis; Ichthyosis, annular epidermolytic, 2; Ichthyosis histrix, Curth-Macklin type; Palmoplantar keratoderma, epidermolytic 2; Palmoplantar keratoderma, nonepidermolytic; Epidermolytic hyperkeratosis 1AD

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

Refs: 14349943; 1381288; 1380725; 7682695; 7528239; 7512983; 10053007; 11286630; 11286616; 12406346; 11982762; 12648226; 16361731; 16417221; 16439967; 16487115; 16677804; 17255957; 18795921; 19470048; 21271994; 21496707; 22250628; 22834809; 30152556Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to KRT1 variants in ClinVar

18 Conditions Cataloged
not providedTotal: 175
Inborn genetic diseasesTotal: 73
KRT1-related disorderTotal: 39
Epidermolytic ichthyosisTotal: 37
Diffuse nonepidermolytic palmoplantar keratodermaTotal: 37
not specifiedTotal: 18
Epidermolytic hyperkeratosis 1Total: 9
Palmoplantar keratoderma, epidermolytic, 2Total: 8

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.

EffectPLPVUSLBBSum
synonymous
4
clinvar
31
clinvar
4
clinvar
39
missense
16
clinvar
19
clinvar
142
clinvar
14
clinvar
2
clinvar
193
nonsense
1
clinvar
2
clinvar
3
start loss
1
clinvar
1
frameshift
8
clinvar
2
clinvar
6
clinvar
16
splice donor/acceptor (+/-2bp)
7
clinvar
2
clinvar
1
clinvar
10
Total3124156456262

Highest pathogenic variant AF is 0.0000020521325

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_006121.4RefSeqNP_006112.39MANE Select
ENST00000252244.3EnsemblENSP00000252244.39MANE 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.2523493630.9630.00002224178
Missense (PolyPhen)96118.950.807081589
Synonymous0.04941421430.9950.000009291333
Loss of Function3.85526.30.1900.00000156288

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.000140.00014rare
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.0000620.000062rare
South Asian0.0000980.000098rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyHighMediumHigh
CancerHighHighHigh
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