KRT20
Basic information
Region (hg38): 17:40875889-40885242
Links
Phenotypes
GenCC
Source:
- schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the KRT20 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 | 4 | |||||
missense | 26 | 30 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 26 | 5 | 3 |
Variants in KRT20
This is a list of pathogenic ClinVar variants found in the KRT20 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
17-40876375-C-T | not specified | Uncertain significance (Feb 23, 2023) | ||
17-40876399-C-T | KRT20-related disorder | Likely benign (Feb 01, 2022) | ||
17-40876402-C-A | not specified | Uncertain significance (May 26, 2024) | ||
17-40876404-T-A | not specified | Uncertain significance (May 18, 2022) | ||
17-40876426-C-T | not specified | Uncertain significance (Jun 28, 2023) | ||
17-40876428-A-G | not specified | Uncertain significance (Sep 20, 2023) | ||
17-40876456-T-C | not specified | Uncertain significance (Feb 28, 2023) | ||
17-40877381-T-G | not specified | Uncertain significance (Mar 20, 2024) | ||
17-40877415-G-T | not specified | Uncertain significance (Jan 12, 2024) | ||
17-40878149-C-T | not specified | Uncertain significance (Dec 16, 2023) | ||
17-40878150-G-A | Benign (Jun 12, 2018) | |||
17-40878242-G-A | not specified | Uncertain significance (Apr 15, 2024) | ||
17-40878274-G-C | not specified | Uncertain significance (Dec 20, 2023) | ||
17-40878290-A-G | Benign (Jul 31, 2018) | |||
17-40878316-C-T | not specified | Uncertain significance (Mar 19, 2024) | ||
17-40878321-G-A | Likely benign (Aug 16, 2018) | |||
17-40879842-C-T | not specified | Uncertain significance (Dec 21, 2022) | ||
17-40879859-C-T | not specified | Uncertain significance (Apr 25, 2023) | ||
17-40879860-G-A | not specified | Uncertain significance (Apr 04, 2024) | ||
17-40879889-C-G | not specified | Uncertain significance (Sep 20, 2023) | ||
17-40880149-A-T | not specified | Uncertain significance (Aug 26, 2022) | ||
17-40880211-A-C | Likely benign (Jun 27, 2018) | |||
17-40880237-G-C | not specified | Uncertain significance (May 26, 2024) | ||
17-40880703-C-G | not specified | Uncertain significance (Nov 09, 2021) | ||
17-40880710-C-G | not specified | Uncertain significance (Jan 23, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
KRT20 | protein_coding | protein_coding | ENST00000167588 | 8 | 9287 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
9.08e-11 | 0.154 | 125645 | 1 | 102 | 125748 | 0.000410 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.369 | 227 | 243 | 0.933 | 0.0000143 | 2774 |
Missense in Polyphen | 72 | 76.911 | 0.93615 | 924 | ||
Synonymous | -0.560 | 104 | 97.0 | 1.07 | 0.00000574 | 821 |
Loss of Function | 0.559 | 17 | 19.7 | 0.864 | 9.85e-7 | 222 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000830 | 0.000824 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000217 | 0.000217 |
Finnish | 0.0000925 | 0.0000924 |
European (Non-Finnish) | 0.000335 | 0.000334 |
Middle Eastern | 0.000217 | 0.000217 |
South Asian | 0.00117 | 0.00105 |
Other | 0.000489 | 0.000489 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a significant role in maintaining keratin filament organization in intestinal epithelia. When phosphorylated, plays a role in the secretion of mucin in the small intestine (By similarity). {ECO:0000250, ECO:0000269|PubMed:12857878, ECO:0000269|PubMed:16608857}.;
- Pathway
- Estrogen signaling pathway - Homo sapiens (human);Keratinization;Developmental Biology
(Consensus)
Recessive Scores
- pRec
- 0.255
Intolerance Scores
- loftool
- 0.210
- rvis_EVS
- 0.18
- rvis_percentile_EVS
- 66.07
Haploinsufficiency Scores
- pHI
- 0.336
- hipred
- N
- hipred_score
- 0.169
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.655
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Krt20
- Phenotype
Gene ontology
- Biological process
- apoptotic process;cellular response to starvation;keratinization;intermediate filament organization;regulation of protein secretion;cornification
- Cellular component
- cytoplasm;cytosol;intermediate filament
- Molecular function
- structural constituent of cytoskeleton;protein binding