KRT16
Basic information
Region (hg38): 17:41609778-41615899
Links
Phenotypes
GenCC
Source:
- pachyonychia congenita 1 (Strong), mode of inheritance: AD
- palmoplantar keratoderma, nonepidermolytic, focal 1 (Strong), mode of inheritance: AD
- pachyonychia congenita 1 (Strong), mode of inheritance: AD
- palmoplantar keratoderma, nonepidermolytic, focal 1 (Moderate), mode of inheritance: AD
- pachyonychia congenita (Supportive), mode of inheritance: AD
- isolated focal non-epidermolytic palmoplantar keratoderma (Supportive), mode of inheritance: AD
- pachyonychia congenita 1 (Strong), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Palmoplantar keratoderma, nonepidermolytic, focal 1; Pachyonychia congenita 1 | AD | General | 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 | Dermatologic | 7544664; 8595410; 10521820; 10839714; 11359398; 11886499; 20301457; 21160496; 21326300; 22098151; 22668561 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (7 variants)
- Pachyonychia congenita 1 (5 variants)
- Palmoplantar keratoderma, nonepidermolytic, focal 1;Pachyonychia congenita 1 (2 variants)
- Palmoplantar keratoderma, nonepidermolytic, focal 1 (2 variants)
- KRT16-related disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRT16 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 20 | 27 | ||||
missense | 29 | 10 | 57 | |||
nonsense | 3 | |||||
start loss | 0 | |||||
frameshift | 3 | |||||
inframe indel | 1 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 3 | 3 | ||||
non coding | 8 | |||||
Total | 7 | 5 | 33 | 36 | 18 |
Highest pathogenic variant AF is 0.00000657
Variants in KRT16
This is a list of pathogenic ClinVar variants found in the KRT16 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
17-41609984-A-G | Palmoplantar keratoderma, nonepidermolytic, focal 1 | Uncertain significance (Feb 02, 2021) | ||
17-41610000-G-A | Likely benign (Aug 27, 2023) | |||
17-41610014-G-A | Benign (Nov 17, 2021) | |||
17-41610044-AGAG-A | Likely benign (Aug 04, 2023) | |||
17-41610193-C-T | Inborn genetic diseases | Uncertain significance (Mar 01, 2024) | ||
17-41610195-C-T | Inborn genetic diseases | Uncertain significance (Nov 23, 2022) | ||
17-41610220-C-T | Inborn genetic diseases | Uncertain significance (Jan 27, 2022) | ||
17-41610252-A-G | Palmoplantar keratoderma, nonepidermolytic, focal 1 • Pachyonychia congenita 1 | Benign (Jan 31, 2024) | ||
17-41610332-G-A | Inborn genetic diseases | Uncertain significance (Jul 13, 2022) | ||
17-41610340-TC-T | not provided (-) | |||
17-41610341-CGCCCTCCAGCAGGCGGCGGTAGGTGG-GCC | Palmoplantar keratoderma, nonepidermolytic, focal 1 | Pathogenic (Jun 01, 2000) | ||
17-41610356-G-A | Likely benign (Aug 04, 2023) | |||
17-41610359-G-A | KRT16-related disorder | Benign (Jan 01, 2024) | ||
17-41610367-G-A | Inborn genetic diseases | Uncertain significance (Oct 07, 2024) | ||
17-41610443-G-A | KRT16-related disorder | Benign/Likely benign (Dec 25, 2023) | ||
17-41610449-G-A | Uncertain significance (Jun 15, 2022) | |||
17-41610494-A-C | Inborn genetic diseases | Likely benign (Mar 28, 2023) | ||
17-41610514-C-T | Likely benign (Jul 20, 2020) | |||
17-41610525-C-A | Uncertain significance (Mar 04, 2022) | |||
17-41610545-A-G | Uncertain significance (May 08, 2023) | |||
17-41610548-C-A | Inborn genetic diseases | Uncertain significance (Sep 02, 2024) | ||
17-41610549-T-A | Pachyonychia congenita 1 • not specified | Conflicting classifications of pathogenicity (Jan 29, 2024) | ||
17-41610556-A-C | Likely benign (Jan 24, 2023) | |||
17-41610924-C-A | Benign (May 31, 2023) | |||
17-41610924-C-T | Uncertain significance (Jun 02, 2017) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
KRT16 | protein_coding | protein_coding | ENST00000301653 | 8 | 6122 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.50e-14 | 0.00697 | 125605 | 0 | 143 | 125748 | 0.000569 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.313 | 294 | 279 | 1.05 | 0.0000190 | 3060 |
Missense in Polyphen | 63 | 75.768 | 0.83148 | 1059 | ||
Synonymous | -2.22 | 153 | 122 | 1.26 | 0.00000846 | 969 |
Loss of Function | -0.458 | 20 | 17.9 | 1.12 | 8.02e-7 | 213 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00532 | 0.00493 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000163 | 0.000163 |
Finnish | 0.000139 | 0.000139 |
European (Non-Finnish) | 0.000368 | 0.000316 |
Middle Eastern | 0.000163 | 0.000163 |
South Asian | 0.0000327 | 0.0000327 |
Other | 0.000507 | 0.000489 |
dbNSFP
Source:
- Function
- FUNCTION: Epidermis-specific type I keratin that plays a key role in skin. Acts as a regulator of innate immunity in response to skin barrier breach: required for some inflammatory checkpoint for the skin barrier maintenance. {ECO:0000250|UniProtKB:Q9Z2K1}.;
- Disease
- DISEASE: Pachyonychia congenita 1 (PC1) [MIM:167200]: An autosomal dominant ectodermal dysplasia characterized by hypertrophic nail dystrophy resulting in onchyogryposis (thickening and increase in curvature of the nail), palmoplantar keratoderma, follicular hyperkeratosis, and oral leukokeratosis. Hyperhidrosis of the hands and feet is usually present. {ECO:0000269|PubMed:10521820, ECO:0000269|PubMed:10606845, ECO:0000269|PubMed:10839714, ECO:0000269|PubMed:11359398, ECO:0000269|PubMed:11886499, ECO:0000269|PubMed:16250206, ECO:0000269|PubMed:17719747, ECO:0000269|PubMed:21160496, ECO:0000269|PubMed:21326300, ECO:0000269|PubMed:22668561, ECO:0000269|PubMed:24118415, ECO:0000269|PubMed:7539673}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Keratoderma, palmoplantar, non-epidermolytic, focal 1 (FNEPPK1) [MIM:613000]: A dermatological disorder characterized by non-epidermolytic palmoplantar keratoderma limited to the pressure points on the balls of the feet, with later mild involvement on the palms. Oral, genital and follicular keratotic lesions are often present. {ECO:0000269|PubMed:8595410}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=KRT16 and KRT17 are coexpressed only in pathological situations such as metaplasias and carcinomas of the uterine cervix and in psoriasis vulgaris.;
- Pathway
- Estrogen signaling pathway - Homo sapiens (human);Vitamin D Receptor Pathway;Keratinization;Developmental Biology
(Consensus)
Recessive Scores
- pRec
- 0.479
Intolerance Scores
- loftool
- 0.120
- rvis_EVS
- 0.64
- rvis_percentile_EVS
- 84.1
Haploinsufficiency Scores
- pHI
- 0.170
- hipred
- N
- hipred_score
- 0.297
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.584
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Krt16
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); digestive/alimentary phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; craniofacial phenotype; cellular phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- morphogenesis of an epithelium;inflammatory response;cytoskeleton organization;aging;cell population proliferation;epidermis development;keratinocyte differentiation;negative regulation of cell migration;keratinization;hair cycle;innate immune response;intermediate filament cytoskeleton organization;keratinocyte migration;establishment of skin barrier;cornification
- Cellular component
- nucleus;cytosol;cytoskeleton;intermediate filament;extracellular exosome
- Molecular function
- structural constituent of cytoskeleton;protein binding