GeneBe

KRT3

keratin 3, the group of Keratins, type II

Basic information

Region (hg38): 12:52789685-52796117

Links

ENSG00000186442 ∙ NCBI:3850 ∙ OMIM:148043 ∙ HGNC:6440 ∙ Uniprot:P12035 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • Meesmann corneal dystrophy (Supportive), mode of inheritance: AD
  • corneal dystrophy, Meesmann, 1 (Strong), mode of inheritance: AD
  • corneal dystrophy, Meesmann, 2 (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.

  • not_specified (94 variants)
  • not_provided (34 variants)
  • KRT3-related_disorder (11 variants)
  • Corneal_dystrophy,_Meesmann,_2 (8 variants)
  • Congenital_hereditary_endothelial_dystrophy_of_cornea (1 variants)

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. These statistics are base on transcript: NM_000057088.3. 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.

EffectPLPVUSLBBSum
synonymous
13
clinvar
4
clinvar
 17
missense
3
clinvar
2
clinvar
96
clinvar
9
clinvar
3
clinvar
 113
nonsense
0
start loss
0
frameshift
1
clinvar
 1
splice donor/acceptor (+/-2bp)
0
Total 3 2 97 22 7

Highest pathogenic variant AF is 0.000011151628

Loading clinvar variants...

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