KRT9
Basic information
Region (hg38): 17:41565836-41572059
Links
Phenotypes
GenCC
Source:
- epidermolytic palmoplantar keratoderma, 1 (Strong), mode of inheritance: AD
- epidermolytic palmoplantar keratoderma, 1 (Strong), mode of inheritance: AD
- epidermolytic palmoplantar keratoderma, 1 (Definitive), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Palmoplantar keratoderma, epidermolytic 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 | 7528239; 7512862; 7511021; 9856842; 12192490; 12838553; 17074468; 19106041 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (95 variants)
- Inborn_genetic_diseases (72 variants)
- Palmoplantar_keratoderma,_epidermolytic (62 variants)
- Epidermolytic_palmoplantar_keratoderma,_1 (23 variants)
- KRT9-related_disorder (12 variants)
- Prostate_cancer (1 variants)
- Palmoplantar_keratoderma (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRT9 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000226.4. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 24 | 33 | ||||
missense | 10 | 103 | 18 | 138 | ||
nonsense | 4 | |||||
start loss | 0 | |||||
frameshift | 2 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 11 | 7 | 114 | 42 | 3 |
Highest pathogenic variant AF is 0.0000030983272
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
KRT9 | protein_coding | protein_coding | ENST00000246662 | 7 | 6215 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00000113 | 0.945 | 125709 | 0 | 39 | 125748 | 0.000155 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.199 | 338 | 348 | 0.970 | 0.0000198 | 4002 |
Missense in Polyphen | 68 | 81.977 | 0.8295 | 1125 | ||
Synonymous | -0.287 | 134 | 130 | 1.03 | 0.00000762 | 1252 |
Loss of Function | 1.84 | 13 | 22.4 | 0.580 | 0.00000113 | 284 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000420 | 0.000420 |
Ashkenazi Jewish | 0.0000992 | 0.0000992 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000152 | 0.000149 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.000368 | 0.000359 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May serve an important special function either in the mature palmar and plantar skin tissue or in the morphogenetic program of the formation of these tissues. Plays a role in keratin filament assembly. {ECO:0000269|PubMed:10218578, ECO:0000269|PubMed:7507869}.;
- Disease
- DISEASE: Keratoderma, palmoplantar, epidermolytic (EPPK) [MIM:144200]: A dermatological disorder characterized by diffuse thickening of the epidermis on the entire surface of palms and soles sharply bordered with erythematous margins. Some patients may present knuckle pads, thick pads of skin appearing over the proximal phalangeal joints. {ECO:0000269|PubMed:10632938, ECO:0000269|PubMed:10844507, ECO:0000269|PubMed:12072061, ECO:0000269|PubMed:12192490, ECO:0000269|PubMed:12838553, ECO:0000269|PubMed:12926810, ECO:0000269|PubMed:14675368, ECO:0000269|PubMed:15099359, ECO:0000269|PubMed:15115518, ECO:0000269|PubMed:15605275, ECO:0000269|PubMed:16911293, ECO:0000269|PubMed:16961539, ECO:0000269|PubMed:19874353, ECO:0000269|PubMed:20964665, ECO:0000269|PubMed:21715251, ECO:0000269|PubMed:7511021, ECO:0000269|PubMed:7512862, ECO:0000269|PubMed:7516304, ECO:0000269|PubMed:7523529, ECO:0000269|PubMed:7532199, ECO:0000269|PubMed:8647270, ECO:0000269|PubMed:9204965, ECO:0000269|PubMed:9856842}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Estrogen signaling pathway - Homo sapiens (human);Keratinization;Developmental Biology
(Consensus)
Recessive Scores
- pRec
- 0.199
Intolerance Scores
- loftool
- 0.109
- rvis_EVS
- -1.2
- rvis_percentile_EVS
- 5.83
Haploinsufficiency Scores
- pHI
- 0.166
- hipred
- N
- hipred_score
- 0.132
- ghis
- 0.431
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.533
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Krt9
- Phenotype
- homeostasis/metabolism phenotype; cellular 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); limbs/digits/tail phenotype; pigmentation phenotype; neoplasm;
Gene ontology
- Biological process
- spermatogenesis;epidermis development;keratinization;skin development;intermediate filament organization;cornification
- Cellular component
- extracellular space;nucleus;cytosol;intermediate filament;membrane;extracellular exosome
- Molecular function
- structural constituent of cytoskeleton