KRT6C

gene
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Summary

KRT6C (keratin 6C, HGNC:20406) is a protein-coding gene on chromosome 12q13.13, encoding Keratin, type II cytoskeletal 6C (P48668).

Keratins are intermediate filament proteins responsible for the structural integrity of epithelial cells and are subdivided into epithelial keratins and hair keratins. The type II keratins are clustered in a region of chromosome 12q13.

Source: NCBI Gene 286887 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): palmoplantar keratoderma, nonepidermolytic, focal or diffuse (Strong, GenCC)
  • Clinical variants (ClinVar): 207 total — 2 pathogenic
  • Phenotypes (HPO): 5
  • MANE Select transcript: NM_173086

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:20406
Approved symbolKRT6C
Namekeratin 6C
Location12q13.13
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000170465
Ensembl biotypeprotein_coding
OMIM612315
Entrez286887

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 retained_intron

ENST00000252250, ENST00000553087

RefSeq mRNA: 1 — MANE Select: NM_173086 NM_173086

CCDS: CCDS8829

Canonical transcript exons

ENST00000252250 — 9 exons

ExonStartEnd
ENSE000016223055247050552470630
ENSE000016342175247206652472280
ENSE000016388945247319852473805
ENSE000016404115246941152469445
ENSE000016662525247167252471732
ENSE000016882025247113252471296
ENSE000017807295247142152471516
ENSE000017893455246967052469890
ENSE000023818695246851652469297

Expression profiles

Bgee: expression breadth broad, 100 present calls, max score 97.87.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 7.2282 / max 2849.9052, expressed in 80 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1310387.149675
1310390.078630

Top tissues by expression

128 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
esophagus mucosaUBERON:000246997.87gold quality
cerebellar vermisUBERON:000472097.41gold quality
lower esophagus mucosaUBERON:003583496.53gold quality
quadriceps femorisUBERON:000137793.41gold quality
thymusUBERON:000237091.12gold quality
vaginaUBERON:000099683.62gold quality
esophagusUBERON:000104373.04gold quality
skin of abdomenUBERON:000141670.04gold quality
ectocervixUBERON:001224966.47gold quality
zone of skinUBERON:000001465.88gold quality
vastus lateralisUBERON:000137964.98gold quality
tonsilUBERON:000237264.24gold quality
skin of legUBERON:000151163.57gold quality
minor salivary glandUBERON:000183062.69gold quality
uterine cervixUBERON:000000261.96gold quality
saliva-secreting glandUBERON:000104460.06gold quality
sural nerveUBERON:001548856.30silver quality
right coronary arteryUBERON:000162555.09gold quality
endocervixUBERON:000045849.62gold quality
olfactory segment of nasal mucosaUBERON:000538648.09gold quality
left uterine tubeUBERON:000130347.23gold quality
right uterine tubeUBERON:000130246.53gold quality
body of pancreasUBERON:000115046.07gold quality
fundus of stomachUBERON:000116045.87gold quality
lower esophagusUBERON:001347345.50gold quality
lower esophagus muscularis layerUBERON:003583345.23gold quality
right lobe of liverUBERON:000111444.78silver quality
left adrenal gland cortexUBERON:003582544.73gold quality
body of stomachUBERON:000116144.57gold quality
left adrenal glandUBERON:000123444.52gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-HCAD-1yes3097.34
E-MTAB-8142yes1267.93
E-GEOD-86618yes9.57
E-MTAB-10596no5900.06
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

40 targeting KRT6C, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-30A-3P99.8769.742928
HSA-MIR-30D-3P99.8769.922917
HSA-MIR-30E-3P99.8769.682942
HSA-MIR-391999.8769.452489
HSA-MIR-4677-5P99.7070.091940
HSA-MIR-3177-5P99.6570.381174
HSA-MIR-7156-5P99.6468.811369
HSA-MIR-80299.6167.701254
HSA-MIR-486-3P99.5166.821901
HSA-MIR-1211799.5067.57868
HSA-MIR-444199.4966.563216
HSA-MIR-361299.4566.021333
HSA-MIR-65099.4565.771309
HSA-MIR-427399.4567.931206
HSA-MIR-127699.3668.181642
HSA-MIR-32-3P99.3668.202517
HSA-MIR-544B99.1867.411632
HSA-MIR-6510-5P99.1466.591081
HSA-MIR-427099.0266.261987
HSA-MIR-6754-5P98.6065.541627
HSA-MIR-31-5P98.5868.351239
HSA-MIR-5581-3P98.5570.311161
HSA-MIR-3928-5P98.5067.48980
HSA-MIR-6806-3P98.5067.31980
HSA-MIR-1212098.0568.441768
HSA-MIR-444398.0266.251928

Literature-anchored findings (GeneRIF, showing 6)

  • Keratin K6c mutations cause focal palmoplantar keratoderma (PMID:19609311)
  • KRT6C mutations may have a role in focal palmoplantar keratoderma [commentary] (PMID:20081885)
  • mutation c.1414G>A resulting in an p.Glu472Lys substitution associated with focal plantar keratoderma (PMID:23662636)
  • report on a novel mutation of KRT6C and highlight the inclusion of focal PPK secondary to KRT16 and KRT6C mutations as a milder phenotype within the spectrum of PC (PMID:26301947)
  • Several missense polymorphisms in KRT6A, KRT6B and KRT6C that lead to a higher risk for dental caries. (PMID:29357356)
  • KRT6C was highly expressed in lung adenocarcinoma (LUAD) patients. The relevance between high expression of KRT6C and poor prognosis of LUAD patients was found in this study. (PMID:31768767)

Cross-species orthologs

8 orthologs

OrganismSymbolGene ID
mus_musculusKrt6bENSMUSG00000023041
mus_musculusKrt6aENSMUSG00000058354
mus_musculusGm5414ENSMUSG00000064232
rattus_norvegicusAABR07001416.1ENSRNOG00000059050
rattus_norvegicusLOC102553726ENSRNOG00000067545
rattus_norvegicusLOC100365213ENSRNOG00000068586
rattus_norvegicusLOC120093742ENSRNOG00000068784
rattus_norvegicusKrt6cENSRNOG00000070470

Paralogs (68): KRT33A (ENSG00000006059), VIM (ENSG00000026025), KRT31 (ENSG00000094796), NEFM (ENSG00000104722), KRT23 (ENSG00000108244), KRT37 (ENSG00000108417), KRT32 (ENSG00000108759), KRT18 (ENSG00000111057), LMNB1 (ENSG00000113368), KRT36 (ENSG00000126337), KRT17 (ENSG00000128422), GFAP (ENSG00000131095), KRT34 (ENSG00000131737), KRT33B (ENSG00000131738), NES (ENSG00000132688), PRPH (ENSG00000135406), KRT85 (ENSG00000135443), KRT7 (ENSG00000135480), KRT71 (ENSG00000139648), INA (ENSG00000148798), LMNTD1 (ENSG00000152936), LMNA (ENSG00000160789), KRT84 (ENSG00000161849), KRT82 (ENSG00000161850), KRT80 (ENSG00000167767), KRT1 (ENSG00000167768), KRT24 (ENSG00000167916), KRT8 (ENSG00000170421), KRT78 (ENSG00000170423), KRT86 (ENSG00000170442), KRT75 (ENSG00000170454), KRT4 (ENSG00000170477), KRT74 (ENSG00000170484), KRT72 (ENSG00000170486), KRT83 (ENSG00000170523), BFSP2 (ENSG00000170819), KRT19 (ENSG00000171345), KRT15 (ENSG00000171346), KRT38 (ENSG00000171360), KRT13 (ENSG00000171401)

Protein

Protein identifiers

Keratin, type II cytoskeletal 6CP48668 (reviewed: P48668)

Alternative names: Cytokeratin-6C, Cytokeratin-6E, Keratin K6h, Keratin-6C, Type-II keratin Kb12

All UniProt accessions (1): P48668

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Heterodimer of a type I and a type II keratin. KRT6 isomers associate with KRT16 and/or KRT17.

Tissue specificity. Constitutively expressed in distinct types of epithelia such as those in oral mucosa, esophagus, papillae of tongue and hair follicle outer root sheath.

Disease relevance. Palmoplantar keratoderma, non-epidermolytic, focal or diffuse (PPKNEFD) [MIM:615735] A dermatological disorder characterized by non-epidermolytic abnormal thickening of the skin on the palms and soles. Diffuse palmoplantar keratoderma is characterized by uniform involvement of the palmoplantar surface, while the focal form consists of localized areas of hyperkeratosis located mainly on pressure points and sites of recurrent friction. The disease is caused by variants affecting the gene represented in this entry.

Miscellaneous. There are at least six isoforms of human type II keratin-6 (K6). There are two types of cytoskeletal and microfibrillar keratin, I (acidic) and II (neutral to basic) (40-55 and 56-70 kDa, respectively).

Similarity. Belongs to the intermediate filament family.

RefSeq proteins (1): NP_775109* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003054Keratin_IIFamily
IPR018039IF_conservedConserved_site
IPR032444Keratin_2_headDomain
IPR039008IF_rod_domDomain

Pfam: PF00038, PF16208

UniProt features (30 total): sequence conflict 10, region of interest 8, sequence variant 5, modified residue 2, initiator methionine 1, chain 1, compositionally biased region 1, site 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P48668-F169.630.40

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 414 (stutter)

Post-translational modifications (2): 2, 60

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-6805567Keratinization
R-HSA-6809371Formation of the cornified envelope
R-HSA-1266738Developmental Biology

MSigDB gene sets: 59 (showing top): GOBP_EPITHELIUM_DEVELOPMENT, GOBP_INTERMEDIATE_FILAMENT_BASED_PROCESS, GU_PDEF_TARGETS_DN, GOBP_INTERMEDIATE_FILAMENT_ORGANIZATION, GCM_PRKCG, GOBP_EPIDERMAL_CELL_DIFFERENTIATION, GCM_RING1, GOBP_EPIDERMIS_DEVELOPMENT, GOBP_KERATINIZATION, GOBP_SKIN_DEVELOPMENT, GCM_LTK, GOCC_INTERMEDIATE_FILAMENT_CYTOSKELETON, GOCC_KERATIN_FILAMENT, GOMF_STRUCTURAL_MOLECULE_ACTIVITY, GCM_FANCC

GO Biological Process (3): keratinization (GO:0031424), intermediate filament cytoskeleton organization (GO:0045104), intermediate filament organization (GO:0045109)

GO Molecular Function (2): structural constituent of skin epidermis (GO:0030280), protein binding (GO:0005515)

GO Cellular Component (4): cytosol (GO:0005829), intermediate filament (GO:0005882), keratin filament (GO:0045095), extracellular exosome (GO:0070062)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Developmental Biology1
Keratinization1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
keratinocyte differentiation1
multicellular organismal process1
cytoskeleton organization1
intermediate filament-based process1
intermediate filament cytoskeleton organization1
supramolecular fiber organization1
structural molecule activity1
binding1
cytoplasm1
cellular anatomical structure1
intermediate filament cytoskeleton1
polymeric cytoskeletal fiber1
intermediate filament1
extracellular vesicle1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

118 interactions, top by confidence:

ABTypeScore
HIF1ANAPBA3psi-mi:“MI:0914”(association)0.850
KRT6CKRT38psi-mi:“MI:0915”(physical association)0.720
KRT31KRT6Cpsi-mi:“MI:0915”(physical association)0.720
KRT6CKRT40psi-mi:“MI:0915”(physical association)0.720
KRT6CTRIM54psi-mi:“MI:0915”(physical association)0.720
KRT38KRT6Cpsi-mi:“MI:0915”(physical association)0.720
KRT40KRT6Cpsi-mi:“MI:0915”(physical association)0.720
KRT6CKRT31psi-mi:“MI:0915”(physical association)0.720
CFTRESYT2psi-mi:“MI:0914”(association)0.710
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
KRT18KRT6Cpsi-mi:“MI:0915”(physical association)0.680
KRT6CKRT13psi-mi:“MI:0915”(physical association)0.560
KRT15KRT6Cpsi-mi:“MI:0915”(physical association)0.560
GOLGA2KRT6Cpsi-mi:“MI:0915”(physical association)0.560
KIFC3KRT6Cpsi-mi:“MI:0915”(physical association)0.560
KRT6CTFIP11psi-mi:“MI:0915”(physical association)0.560
KRT13KRT6Cpsi-mi:“MI:0915”(physical association)0.560
KRT6CKRT15psi-mi:“MI:0915”(physical association)0.560
KRT6CGOLGA2psi-mi:“MI:0915”(physical association)0.560

BioGRID (99): KRT6C (Two-hybrid), KRT6C (Two-hybrid), KRT6C (Two-hybrid), KRT6C (Two-hybrid), KRT6C (Two-hybrid), KRT6C (Two-hybrid), KRT6C (Two-hybrid), KRT6C (Two-hybrid), KRT6C (Two-hybrid), KRT6C (Affinity Capture-MS), KRT6C (Affinity Capture-MS), KRT6C (Affinity Capture-MS), KRT6C (Affinity Capture-MS), KRT6C (Two-hybrid), KRT6C (Affinity Capture-MS)

ESM2 similar proteins: A5A6M6, A5A6M8, O95678, P02535, P02537, P02538, P04104, P04259, P04264, P06394, P07744, P08776, P12035, P13645, P13647, P16878, P18520, P19013, P35527, P35908, P48668, P50446, Q01546, Q08D91, Q148H7, Q29426, Q2M2I5, Q3TTY5, Q3UV17, Q4FZU2, Q5XQN5, Q6EIY9, Q6EIZ0, Q6EIZ1, Q6IFW6, Q6IFZ6, Q6IG00, Q6IG01, Q6IG02, Q6IG05

Diamond homologs: A0A8C0N8E3, A5A6M8, A5A6N0, A6QQJ3, B4F721, O62654, O77788, O93532, O95678, P02538, P02540, P02541, P02542, P02543, P02544, P02547, P02548, P03995, P04259, P05786, P05787, P07196, P07197, P08551, P08552, P08553, P08670, P08729, P08776, P09654, P11679, P12035, P12036, P12839, P13647, P14136, P15331, P16053, P16878, P16884

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 70 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Formation of the cornified envelope1931.5×6e-22
Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin526.3×7e-05
Keratinization1818.9×8e-17

GO biological processes:

GO termPartnersFoldFDR
morphogenesis of an epithelium1790.0×3e-27
intermediate filament organization1866.7×1e-26
epithelial cell differentiation1540.5×2e-18

Disease & clinical

Clinical variants and AI predictions

ClinVar

207 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic2
Likely pathogenic0
Uncertain significance114
Likely benign42
Benign34

Top pathogenic / likely-pathogenic (2)

Variant IDHGVSClassification
126525NM_173086.5(KRT6C):c.510CAA[2] (p.Asn172del)Pathogenic
66966NM_173086.5(KRT6C):c.1384_1410del (p.Ile462_Glu470del)Pathogenic

SpliceAI

595 predictions. Top by Δscore:

VariantEffectΔscore
12:52469405:ACTT:Adonor_loss1.0000
12:52469408:TACA:Tdonor_loss1.0000
12:52469409:A:ACdonor_gain1.0000
12:52469409:ACAG:Adonor_loss1.0000
12:52469410:C:CTdonor_gain1.0000
12:52469410:CAG:Cdonor_gain1.0000
12:52469410:CAGA:Cdonor_gain1.0000
12:52469444:GCCT:Gacceptor_loss1.0000
12:52469445:CCTGT:Cacceptor_loss1.0000
12:52469446:C:CAacceptor_loss1.0000
12:52469446:C:CCacceptor_gain1.0000
12:52469447:T:Aacceptor_loss1.0000
12:52469666:CTA:Cdonor_loss1.0000
12:52469668:A:ACdonor_gain1.0000
12:52469669:C:CCdonor_gain1.0000
12:52469669:C:CTdonor_loss1.0000
12:52469669:CCTG:Cdonor_gain1.0000
12:52469887:CACA:Cacceptor_gain1.0000
12:52469889:CA:Cacceptor_gain1.0000
12:52469891:C:CCacceptor_gain1.0000
12:52470631:C:CCacceptor_gain1.0000
12:52470639:C:CTacceptor_gain1.0000
12:52470640:A:Tacceptor_gain1.0000
12:52471128:TCA:Tdonor_loss1.0000
12:52471129:CACCT:Cdonor_loss1.0000
12:52471153:AG:Adonor_gain1.0000
12:52471197:TG:Tdonor_gain1.0000
12:52471292:AGCTC:Aacceptor_gain1.0000
12:52471293:GCTC:Gacceptor_gain1.0000
12:52471294:CTC:Cacceptor_gain1.0000

AlphaMissense

3690 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:52470620:A:GL363P0.999
12:52473216:A:CF174L0.999
12:52473216:A:TF174L0.999
12:52473217:A:CF174C0.999
12:52473217:A:GF174S0.999
12:52473218:A:GF174L0.999
12:52469860:C:GA412P0.998
12:52471155:C:GA352P0.998
12:52471163:C:GR349P0.998
12:52471176:C:GA345P0.998
12:52471675:C:AK271N0.998
12:52471675:C:GK271N0.998
12:52472249:A:GL191P0.998
12:52473225:G:CN171K0.998
12:52473225:G:TN171K0.998
12:52469827:C:GA423P0.997
12:52470587:A:GL374P0.997
12:52471250:A:GL320P0.997
12:52471250:A:TL320Q0.997
12:52472261:T:GQ187P0.997
12:52472270:A:GL184P0.997
12:52473214:G:TA175D0.997
12:52473226:T:AN171I0.997
12:52473229:A:GL170P0.997
12:52469721:A:GL458P0.996
12:52471165:G:CS348R0.996
12:52471165:G:TS348R0.996
12:52471167:T:GS348R0.996
12:52471175:G:TA345D0.996
12:52471188:A:GY341H0.996

dbSNP variants (sampled 300 via entrez): RS1000113268 (12:52470936 T>G), RS1001579291 (12:52470292 C>T), RS1003101883 (12:52475311 C>A,T), RS1003108179 (12:52474720 G>A,C), RS1003172279 (12:52468513 G>A), RS1003310714 (12:52468424 G>C), RS1003401956 (12:52474474 A>C,T), RS1003466850 (12:52473508 C>T), RS1004148335 (12:52473984 A>T), RS1004259875 (12:52474154 G>A), RS1004482773 (12:52472497 C>T), RS1004597273 (12:52473024 G>A,C), RS1006468056 (12:52474982 A>G), RS1007439716 (12:52471944 C>T), RS10083103 (12:52468081 G>A)

Disease associations

OMIM: gene MIM:612315 | disease phenotypes: MIM:615735

GenCC curated gene-disease

DiseaseClassificationInheritance
palmoplantar keratoderma, nonepidermolytic, focal or diffuseStrongAutosomal dominant

Mondo (2): focal palmoplantar keratoderma (MONDO:0017672), palmoplantar keratoderma, nonepidermolytic, focal or diffuse (MONDO:0014327)

Orphanet (2): Focal palmoplantar keratoderma (Orphanet:307837), Autosomal dominant focal non-epidermolytic palmoplantar keratoderma with plantar blistering (Orphanet:402003)

HPO phenotypes

5 total (5 of 5 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000982Palmoplantar keratoderma
HP:0002745Oral leukoplakia
HP:0007556Plantar hyperkeratosis
HP:0025092Epidermal acanthosis

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

ChemicalActions (top 5)PubMed papers
chloropicrinaffects expression, decreases expression2
Potassium Dichromatedecreases expression2
Aflatoxin B1decreases methylation, increases expression2
Cadmium Chloridedecreases expression, increases expression2
sodium arsenitedecreases expression1
isobutyl alcoholincreases abundance, increases expression, affects cotreatment1
4-((3-bromophenyl)amino)-6,7-dimethoxyquinazolineaffects cotreatment, decreases expression1
CGP 52608affects binding, increases reaction1
2-palmitoylglycerolincreases expression1
Troglitazoneaffects cotreatment, decreases expression, increases expression1
Ethanolaffects cotreatment, increases abundance, increases expression1
Benzo(a)pyreneincreases methylation1
Cadmiumaffects binding1
Dichlorodiphenyl Dichloroethylenedecreases expression1
Dinitrochlorobenzeneaffects binding1
Estradioldecreases expression1
Gasolineincreases abundance, increases expression, affects cotreatment1
Ivermectindecreases expression1
Leadaffects binding1
Nickelaffects binding1
Phenobarbitalaffects expression1
Polycyclic Aromatic Hydrocarbonsaffects cotreatment, increases abundance, increases expression1
Tobacco Smoke Pollutionincreases expression1
Okadaic Acidincreases expression1
Copper Sulfatedecreases expression1
1-Butanolaffects cotreatment, increases abundance, increases expression1
Particulate Matteraffects cotreatment, increases abundance, increases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.