GeneBe

KRT3

protein-coding

keratin 3, the group of Keratins, type II

Gene summary

The protein encoded by this gene is a member of the keratin gene family. The type II cytokeratins consist of basic or neutral proteins which are arranged in pairs of heterotypic keratin chains coexpressed during differentiation of simple and stratified epithelial tissues. This type II cytokeratin is specifically expressed in the corneal epithelium with family member KRT12 and mutations in these genes have been associated with Meesmann's Corneal Dystrophy. The type II cytokeratins are clustered in a region of chromosome 12q12-q13. [provided by RefSeq, Jul 2008]

MANE transcript

NM_057088.3

Inheritance

AD

ClinVar variants

P:5U:111B:50

Top phenotype

Corneal dystrophy, Meesmann, 2

gnomAD constraint

pLI —, LoF o/e 0.81

Max pathogenic AF

—

Genomic locus

chr12:52,789,685-52,796,117

External References & Databases

Ensembl (ENSG00000186442)NCBI Gene (3850)OMIM (148043)HGNC:6440GenCCUniProt (P12035)AlphaFoldClinVar (KRT3)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~6.4 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

corneal dystrophy, Meesmann, 2STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0032904

Submitter: PanelApp Australia

corneal dystrophy, Meesmann, 1STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0020791

Submitter: Labcorp Genetics (formerly Invitae)

corneal dystrophy, Meesmann, 2STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0032904

Submitter: G2P

Meesmann corneal dystrophySUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007379

Submitter: Orphanet

Clinical Genomic Database (CGD)

Corneal dystrophy, Meesmann, 2AD

Manifestation: Ophthalmologic

Intervention: General

Rationale: 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

Refs: 9171831Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to KRT3 variants in ClinVar

5 Conditions Cataloged
not specifiedTotal: 116
not providedTotal: 56
KRT3-related disorderTotal: 12
Corneal dystrophy, Meesmann, 2Total: 8
Congenital hereditary endothelial dystrophy of corneaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_057088.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
4
clinvar
24
clinvar
6
clinvar
 34
missense
2
clinvar
3
clinvar
106
clinvar
15
clinvar
5
clinvar
 131
nonsense
0
start loss
0
frameshift
1
clinvar
 1
splice donor/acceptor (+/-2bp)
0
Total231113911166

Highest pathogenic variant AF is 0.000011151628

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_057088.3RefSeqNP_476429.29MANE Select
ENST00000417996.2EnsemblENSP00000413479.29MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Keratinization
  • Developmental Biology

Biological Process

  • epithelial cell differentiation
  • keratinization
  • intermediate filament cytoskeleton organization
  • cornification

Molecular Function

  • structural molecule activity

Cellular Component

  • cytosol
  • intermediate filament
  • keratin filament
  • extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000417996
Coding exons
9
Length
6433
Individuals with no LoFs
125674
Homozygous LoFs
1
Heterozygous LoFs
73
Defined
125748
p
0.000294
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.06803693730.9900.00002264073
Missense (PolyPhen)100109.080.916731513
Synonymous-1.541791551.160.00001011298
Loss of Function0.7781619.70.8118.44e-7245

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000380.00037rare
Latino/Admixed American0.000510.00046rare
Ashkenazi Jewish00.0absent
East Asian0.00100.0010notable
Finnish00.0absent
European (Non-Finnish)0.000190.00018rare
South Asian0.000390.00036rare
Other0.000160.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool
0.164
RVIS EVS
0.38
RVIS percentile EVS
75.65

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.180

Gene Damage Prediction

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh
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