KRT3
Basic information
Region (hg38): 12:52789685-52796117
Links
Phenotypes
GenCC
Source:
- Meesmann corneal dystrophy (Supportive), mode of inheritance: AD
- corneal dystrophy, Meesmann, 1 (Strong), mode of inheritance: AD
- corneal dystrophy, Meesmann, 1 (Strong), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Corneal dystrophy, Meesmann, 2 | 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 | Ophthalmologic | 9171831 |
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 KRT3 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 | 11 | 17 | ||||
missense | 37 | 52 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 2 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region | 1 | 2 | 3 | |||
non coding | 1 | |||||
Total | 0 | 2 | 37 | 16 | 18 |
Variants in KRT3
This is a list of pathogenic ClinVar variants found in the KRT3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
12-52790076-T-A | not specified | Uncertain significance (Dec 30, 2023) | ||
12-52790088-A-T | not specified | Uncertain significance (Aug 12, 2024) | ||
12-52790098-C-T | Benign (Nov 10, 2023) | |||
12-52790102-G-A | Likely benign (Nov 15, 2023) | |||
12-52790111-C-T | Benign (Jan 14, 2023) | |||
12-52790127-C-T | KRT3-related disorder | Likely benign (Sep 19, 2023) | ||
12-52790167-C-CGCTGCCACCGCTGAAACCGCT | Benign (Jan 29, 2024) | |||
12-52790176-C-T | not specified | Uncertain significance (Sep 16, 2021) | ||
12-52790205-C-T | not specified | Uncertain significance (Nov 27, 2024) | ||
12-52790219-A-G | Likely benign (Jun 08, 2018) | |||
12-52790221-C-T | not specified | Likely benign (Aug 19, 2023) | ||
12-52790232-C-G | not specified | Uncertain significance (Mar 20, 2024) | ||
12-52790259-C-T | not specified | Uncertain significance (Jan 19, 2022) | ||
12-52790265-C-A | not specified | Uncertain significance (Dec 13, 2022) | ||
12-52790268-A-C | not specified | Uncertain significance (Aug 11, 2022) | ||
12-52790272-C-T | not specified | Uncertain significance (Dec 19, 2022) | ||
12-52790276-T-C | Benign (Mar 21, 2023) | |||
12-52790289-C-T | not specified | Uncertain significance (Jul 14, 2021) | ||
12-52790292-A-G | not specified | Uncertain significance (Apr 07, 2023) | ||
12-52790302-C-G | not specified | Uncertain significance (May 01, 2024) | ||
12-52790355-A-G | not specified | Uncertain significance (Oct 25, 2023) | ||
12-52790363-G-C | KRT3-related disorder | Benign (Jun 07, 2019) | ||
12-52790835-T-TA | Benign (Jan 29, 2024) | |||
12-52791200-G-A | Benign (Nov 15, 2018) | |||
12-52791214-C-A | Corneal dystrophy, Meesmann, 2 | Likely pathogenic (Jan 01, 2021) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
KRT3 | protein_coding | protein_coding | ENST00000417996 | 9 | 6433 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
9.00e-10 | 0.289 | 125674 | 1 | 73 | 125748 | 0.000294 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.0680 | 369 | 373 | 0.990 | 0.0000226 | 4073 |
Missense in Polyphen | 100 | 109.08 | 0.91673 | 1513 | ||
Synonymous | -1.54 | 179 | 155 | 1.16 | 0.0000101 | 1298 |
Loss of Function | 0.778 | 16 | 19.7 | 0.811 | 8.44e-7 | 245 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000890 | 0.000882 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00104 | 0.00103 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000189 | 0.000185 |
Middle Eastern | 0.00104 | 0.00103 |
South Asian | 0.000393 | 0.000359 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Pathway
- Keratinization;Developmental Biology
(Consensus)
Intolerance Scores
- loftool
- 0.164
- rvis_EVS
- 0.38
- rvis_percentile_EVS
- 75.65
Haploinsufficiency Scores
- pHI
- 0.155
- hipred
- N
- hipred_score
- 0.112
- ghis
- 0.414
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.180
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | High | High | High |
Primary Immunodeficiency | High | High | High |
Cancer | High | High | High |
Gene ontology
- Biological process
- epithelial cell differentiation;keratinization;intermediate filament cytoskeleton organization;cornification
- Cellular component
- cytosol;intermediate filament;keratin filament;extracellular exosome
- Molecular function
- structural molecule activity