KRT20

keratin 20, the group of Keratins, type I

Basic information

Region (hg38): 17:40875889-40885242

Links

ENSG00000171431NCBI:54474OMIM:608218HGNC:20412Uniprot:P35900AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KRT20 gene.

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
2
clinvar
2
clinvar
4
missense
26
clinvar
3
clinvar
1
clinvar
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)3116371
17-40876399-C-T KRT20-related disorder Likely benign (Feb 01, 2022)3038166
17-40876402-C-A not specified Uncertain significance (May 26, 2024)2346277
17-40876404-T-A not specified Uncertain significance (May 18, 2022)2290341
17-40876426-C-T not specified Uncertain significance (Jun 28, 2023)2592117
17-40876428-A-G not specified Uncertain significance (Sep 20, 2023)3116370
17-40876456-T-C not specified Uncertain significance (Feb 28, 2023)2490952
17-40877381-T-G not specified Uncertain significance (Mar 20, 2024)3289361
17-40877415-G-T not specified Uncertain significance (Jan 12, 2024)3116369
17-40878149-C-T not specified Uncertain significance (Dec 16, 2023)3116368
17-40878150-G-A Benign (Jun 12, 2018)711187
17-40878242-G-A not specified Uncertain significance (Apr 15, 2024)3289360
17-40878274-G-C not specified Uncertain significance (Dec 20, 2023)3116367
17-40878290-A-G Benign (Jul 31, 2018)777163
17-40878316-C-T not specified Uncertain significance (Mar 19, 2024)3289364
17-40878321-G-A Likely benign (Aug 16, 2018)764910
17-40879842-C-T not specified Uncertain significance (Dec 21, 2022)2409315
17-40879859-C-T not specified Uncertain significance (Apr 25, 2023)2540012
17-40879860-G-A not specified Uncertain significance (Apr 04, 2024)3289365
17-40879889-C-G not specified Uncertain significance (Sep 20, 2023)3116377
17-40880149-A-T not specified Uncertain significance (Aug 26, 2022)2221776
17-40880211-A-C Likely benign (Jun 27, 2018)755295
17-40880237-G-C not specified Uncertain significance (May 26, 2024)3289366
17-40880703-C-G not specified Uncertain significance (Nov 09, 2021)2260106
17-40880710-C-G not specified Uncertain significance (Jan 23, 2023)2463983

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
KRT20protein_codingprotein_codingENST00000167588 89287
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
9.08e-110.15412564511021257480.000410
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.3692272430.9330.00001432774
Missense in Polyphen7276.9110.93615924
Synonymous-0.56010497.01.070.00000574821
Loss of Function0.5591719.70.8649.85e-7222

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0008300.000824
Ashkenazi Jewish0.000.00
East Asian0.0002170.000217
Finnish0.00009250.0000924
European (Non-Finnish)0.0003350.000334
Middle Eastern0.0002170.000217
South Asian0.001170.00105
Other0.0004890.000489

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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