KRT3

keratin 3, the group of Keratins, type II

Basic information

Region (hg38): 12:52789685-52796117

Links

ENSG00000186442NCBI:3850OMIM:148043HGNC:6440Uniprot:P12035AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • 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: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Corneal dystrophy, Meesmann, 2ADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingOphthalmologic9171831

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KRT3 gene.

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
clinvar
6
clinvar
17
missense
2
clinvar
37
clinvar
5
clinvar
8
clinvar
52
nonsense
0
start loss
0
frameshift
0
inframe indel
2
clinvar
2
splice donor/acceptor (+/-2bp)
1
clinvar
1
splice region
1
2
3
non coding
1
clinvar
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)3116439
12-52790088-A-T not specified Uncertain significance (Aug 12, 2024)3535964
12-52790098-C-T Benign (Nov 10, 2023)725616
12-52790102-G-A Likely benign (Nov 15, 2023)2726307
12-52790111-C-T Benign (Jan 14, 2023)2715133
12-52790127-C-T KRT3-related disorder Likely benign (Sep 19, 2023)2059950
12-52790167-C-CGCTGCCACCGCTGAAACCGCT Benign (Jan 29, 2024)768550
12-52790176-C-T not specified Uncertain significance (Sep 16, 2021)2405991
12-52790205-C-T not specified Uncertain significance (Nov 27, 2024)3535959
12-52790219-A-G Likely benign (Jun 08, 2018)718343
12-52790221-C-T not specified Likely benign (Aug 19, 2023)2619353
12-52790232-C-G not specified Uncertain significance (Mar 20, 2024)3289403
12-52790259-C-T not specified Uncertain significance (Jan 19, 2022)2271656
12-52790265-C-A not specified Uncertain significance (Dec 13, 2022)2334250
12-52790268-A-C not specified Uncertain significance (Aug 11, 2022)2371167
12-52790272-C-T not specified Uncertain significance (Dec 19, 2022)2271069
12-52790276-T-C Benign (Mar 21, 2023)2702151
12-52790289-C-T not specified Uncertain significance (Jul 14, 2021)2204788
12-52790292-A-G not specified Uncertain significance (Apr 07, 2023)2535281
12-52790302-C-G not specified Uncertain significance (May 01, 2024)3289398
12-52790355-A-G not specified Uncertain significance (Oct 25, 2023)3116437
12-52790363-G-C KRT3-related disorder Benign (Jun 07, 2019)3044013
12-52790835-T-TA Benign (Jan 29, 2024)2033335
12-52791200-G-A Benign (Nov 15, 2018)709653
12-52791214-C-A Corneal dystrophy, Meesmann, 2 Likely pathogenic (Jan 01, 2021)2628033

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
KRT3protein_codingprotein_codingENST00000417996 96433
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
9.00e-100.2891256741731257480.000294
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.06803693730.9900.00002264073
Missense in Polyphen100109.080.916731513
Synonymous-1.541791551.160.00001011298
Loss of Function0.7781619.70.8118.44e-7245

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0008900.000882
Ashkenazi Jewish0.000.00
East Asian0.001040.00103
Finnish0.000.00
European (Non-Finnish)0.0001890.000185
Middle Eastern0.001040.00103
South Asian0.0003930.000359
Other0.0001630.000163

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh

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