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 m... See more...

Aliases for KRT3 Gene

Aliases for KRT3 Gene

  • Keratin 3 2 3 5
  • Keratin, Type II Cytoskeletal 3 2 3 4
  • K3 2 3 4
  • Type-II Keratin Kb3 3 4
  • 65 KDa Cytokeratin 3 4
  • Cytokeratin 3 2 3
  • CK-3 3 4
  • CK3 2 3
  • Keratin 3, Type II 3
  • Cytokeratin-3 4
  • Keratin-3 4
  • MECD2 3
  • KRT3 5

External Ids for KRT3 Gene

Previous GeneCards Identifiers for KRT3 Gene

  • GC12M053297
  • GC12P053675
  • GC12M052626
  • GC12M051469
  • GC12M053183
  • GC12M050227

Summaries for KRT3 Gene

Entrez Gene Summary for KRT3 Gene

  • 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]

GeneCards Summary for KRT3 Gene

KRT3 (Keratin 3) is a Protein Coding gene. Diseases associated with KRT3 include Corneal Dystrophy, Meesmann, 2 and Corneal Dystrophy, Meesmann, 1. Among its related pathways are Developmental Biology and Keratinization. Gene Ontology (GO) annotations related to this gene include structural molecule activity. An important paralog of this gene is KRT76.

Gene Wiki entry for KRT3 Gene

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for KRT3 Gene

Genomics for KRT3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for KRT3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J052805 Enhancer 0.6 Ensembl ENCODE 610.1 +0.3 263 1.1 FOXA1 SPI1 ZNF384 MNT KRT3 HSALNG0091205 KRT76
GH12J052796 Promoter 0.3 EPDnew 600.4 +9.6 9598 0.1 KRT3 HSALNG0091205 KRT76
GH12J052799 Enhancer 1.1 Ensembl ENCODE 10.2 +6.7 6734 5.6 HNRNPL ARID3A REST LEF1 IKZF1 TARDBP JUND FOXA1 MTA2 ZIC2 KRT3 HSALNG0091205 KRT76
GH12J052869 Enhancer 1.6 FANTOM5 ENCODE CraniofacialAtlas dbSUPER 5.1 -67.6 -67590 7.1 CTCF PRDM10 ZNF629 LEF1 IKZF1 ZNF692 TARDBP JUND FOXA1 PRDM1 lnc-KRT8-2 KRT2 AAAS KRT84 ZNF740 PFDN5 KRT79 TARBP2 ENSG00000257808 CSAD
GH12J052840 Enhancer 0.4 Ensembl 10.6 -36.7 -36666 3.2 GLIS1 EGR2 SREBF1 piR-43105-122 KRT4 KRT3 KRT76 KRT1 KRT84 KRT83 OR7E47P AMHR2 KRT78
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around KRT3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for KRT3

Top Transcription factor binding sites by QIAGEN in the KRT3 gene promoter:
  • AML1a
  • AP-4
  • E47
  • p300
  • p53
  • PPAR-alpha
  • RFX1
  • STAT3
  • Tal-1beta
  • YY1

Genomic Locations for KRT3 Gene

Genomic Locations for KRT3 Gene
16,051 bases
Minus strand
6,433 bases
Minus strand

Genomic View for KRT3 Gene

Genes around KRT3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
KRT3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for KRT3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KRT3 Gene

Proteins for KRT3 Gene

  • Protein details for KRT3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Keratin, type II cytoskeletal 3
    Protein Accession:
    Secondary Accessions:
    • A6NIS2
    • Q701L8

    Protein attributes for KRT3 Gene

    628 amino acids
    Molecular mass:
    64417 Da
    Quaternary structure:
    • Heterotetramer of two type I and two type II keratins. Keratin-3 associates with keratin-12.
    • Sequence=CAF31522.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
    • There are two types of cytoskeletal and microfibrillar keratin: I (acidic; 40-55 kDa) and II (neutral to basic; 56-70 kDa).

neXtProt entry for KRT3 Gene

Post-translational modifications for KRT3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for KRT3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for KRT3 Gene

Domains & Families for KRT3 Gene

Gene Families for KRT3 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for KRT3 Gene

  • Intermediate filament protein
  • Type I keratin signature
  • Protein kinase PKN/PRK1, effector
  • Type II keratin signature

Suggested Antigen Peptide Sequences for KRT3 Gene

GenScript: Design optimal peptide antigens:
  • Type-II keratin Kb3 (K2C3_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the intermediate filament family.
  • Belongs to the intermediate filament family.
genes like me logo Genes that share domains with KRT3: view

Function for KRT3 Gene

Molecular function for KRT3 Gene

GENATLAS Biochemistry:
keratin 3,type II (64kDa),expressed during corneal differentiation
genes like me logo Genes that share phenotypes with KRT3: view

Animal Model Products

CRISPR Products

miRNA for KRT3 Gene

miRTarBase miRNAs that target KRT3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for KRT3

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for KRT3 Gene

Localization for KRT3 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for KRT3 gene
Compartment Confidence
cytoskeleton 5
extracellular 4
cytosol 4
nucleus 3
plasma membrane 2
mitochondrion 1
endoplasmic reticulum 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for KRT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
GO:0005882 intermediate filament NAS 9171831
GO:0045095 keratin filament TAS 9171831
GO:0070062 extracellular exosome HDA 23533145
genes like me logo Genes that share ontologies with KRT3: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for KRT3 Gene

Pathways & Interactions for KRT3 Gene

PathCards logo

SuperPathways for KRT3 Gene

SuperPathway Contained pathways
1 Developmental Biology
2 Keratinization
genes like me logo Genes that share pathways with KRT3: view

Pathways by source for KRT3 Gene

2 Reactome pathways for KRT3 Gene

Gene Ontology (GO) - Biological Process for KRT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030855 epithelial cell differentiation ISS --
GO:0031424 keratinization TAS --
GO:0045104 intermediate filament cytoskeleton organization IMP 9171831
GO:0070268 cornification TAS --
genes like me logo Genes that share ontologies with KRT3: view

No data available for SIGNOR curated interactions for KRT3 Gene

Drugs & Compounds for KRT3 Gene

(4) Drugs for KRT3 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with KRT3: view

Transcripts for KRT3 Gene

mRNA/cDNA for KRT3 Gene

4 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for KRT3

Alternative Splicing Database (ASD) splice patterns (SP) for KRT3 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8
SP2: - - - - - - -

Relevant External Links for KRT3 Gene

GeneLoc Exon Structure for

Expression for KRT3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for KRT3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for KRT3 Gene

This gene is overexpressed in Esophagus - Mucosa (x24.6), Minor Salivary Gland (x6.0), Vagina (x5.2), and Cervix - Ectocervix (x4.4).

Protein differential expression in normal tissues from HIPED for KRT3 Gene

This gene is overexpressed in Saliva (39.0) and Cervix (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for KRT3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for KRT3

SOURCE GeneReport for Unigene cluster for KRT3 Gene:


mRNA Expression by UniProt/SwissProt for KRT3 Gene:

Tissue specificity: Cornea specific.

Evidence on tissue expression from TISSUES for KRT3 Gene

  • Eye(4.7)
  • Intestine(2.7)
  • Lung(2.6)
  • Heart(2.5)
  • Blood(2.3)
  • Liver(2.2)
  • Nervous system(2.1)
  • Skin(2.1)
  • Kidney(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for KRT3 Gene

Germ Layers:
  • ectoderm
  • nervous
Head and neck:
  • eye
  • head
genes like me logo Genes that share expression patterns with KRT3: view

Primer Products

No data available for Protein tissue co-expression partners for KRT3 Gene

Orthologs for KRT3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for KRT3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia KRT3 31
  • 98 (a)
(Bos Taurus)
Mammalia KRT3 31
  • 84 (a)
(Canis familiaris)
Mammalia KRT3 31
  • 80 (a)
(Monodelphis domestica)
Mammalia -- 31
  • 76 (a)
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 73 (a)
(Mus musculus)
Mammalia 4732456N10Rik 31
  • 59 (a)
(Gallus gallus)
Aves -- 31
  • 62 (a)
(Anolis carolinensis)
Reptilia -- 31
  • 59 (a)
Species where no ortholog for KRT3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for KRT3 Gene

Gene Tree for KRT3 (if available)
Gene Tree for KRT3 (if available)
Evolutionary constrained regions (ECRs) for KRT3: view image

Paralogs for KRT3 Gene Pseudogenes for KRT3 Gene

genes like me logo Genes that share paralogs with KRT3: view

Variants for KRT3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for KRT3 Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
709653 Benign: not provided 52,791,200(-) G/A INTRON_VARIANT
718343 Likely Benign: not provided 52,790,219(-) A/G SYNONYMOUS_VARIANT
725616 Benign: not provided 52,790,098(-) C/T MISSENSE_VARIANT
726602 Benign: not provided 52,792,738(-) G/A SYNONYMOUS_VARIANT
730710 Benign: not provided 52,794,271(-) G/C MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for KRT3 Gene

Structural Variations from Database of Genomic Variants (DGV) for KRT3 Gene

Variant ID Type Subtype PubMed ID
esv3446771 CNV insertion 20981092
esv3629524 CNV gain 21293372
nsv832416 CNV loss 17160897
nsv975494 CNV duplication 23825009

Variation tolerance for KRT3 Gene

Residual Variation Intolerance Score: 93% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 17.50; 98.22% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for KRT3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for KRT3 Gene

Disorders for KRT3 Gene

MalaCards: The human disease database

(45) MalaCards diseases for KRT3 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, Orphanet, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search KRT3 in MalaCards View complete list of genes associated with diseases


  • Corneal dystrophy, Meesmann 2 (MECD2) [MIM:618767]: A form of Meesmann corneal dystrophy, a corneal disease characterized by fragility of the anterior corneal epithelium. Histological examination shows a disorganized and thickened epithelium with widespread cytoplasmic vacuolation and numerous small, round, debris-laden intraepithelial cysts. Patients are usually asymptomatic until adulthood when rupture of the corneal microcysts may cause erosions, producing clinical symptoms such as photophobia, contact lens intolerance and intermittent diminution of visual acuity. Rarely, subepithelial scarring causes irregular corneal astigmatism and permanent visual impairment. MECD2 inheritance is autosomal dominant. {ECO:0000269 PubMed:16227835, ECO:0000269 PubMed:9171831}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for KRT3

genes like me logo Genes that share disorders with KRT3: view

No data available for Genatlas for KRT3 Gene

Publications for KRT3 Gene

  1. Novel mutations in the helix termination motif of keratin 3 and keratin 12 in 2 Taiwanese families with Meesmann corneal dystrophy. (PMID: 16227835) Chen YT … Chao SC (Cornea 2005) 3 4 23
  2. Assignment of the human cytokeratin 3 gene (KRT3) to 12q12-->q13 by FISH. (PMID: 7510223) Raimondi E … Romano V (Cytogenetics and cell genetics 1994) 2 3 23
  3. Genetics of Meesmann corneal dystrophy: a novel mutation in the keratin 3 gene in an asymptomatic family suggests genotype-phenotype correlation. (PMID: 18806880) Szaflik JP … Szaflik J (Molecular vision 2008) 3 23
  4. New consensus nomenclature for mammalian keratins. (PMID: 16831889) Schweizer J … Wright MW (The Journal of cell biology 2006) 2 3
  5. Characterization of new members of the human type II keratin gene family and a general evaluation of the keratin gene domain on chromosome 12q13.13. (PMID: 15737194) Rogers MA … Schweizer J (The Journal of investigative dermatology 2005) 3 4

Products for KRT3 Gene

Sources for KRT3 Gene