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Atlas / Gene / KRT23

KRT23

gene
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Also known as K23DKFZP434G032HAIK1CK23MGC26158

Summary

KRT23 (keratin 23, HGNC:6438) is a protein-coding gene on chromosome 17q21.2, encoding Keratin, type I cytoskeletal 23 (Q9C075).

The protein encoded by this gene is a member of the keratin family. The keratins are intermediate filament proteins responsible for the structural integrity of epithelial cells and are subdivided into cytokeratins and hair keratins. The type I cytokeratins consist of acidic proteins which are arranged in pairs of heterotypic keratin chains. The type I cytokeratin genes are clustered in a region of chromosome 17q12-q21. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 25984 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 75 total
  • MANE Select transcript: NM_015515

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:6438
Approved symbolKRT23
Namekeratin 23
Location17q21.2
Locus typegene with protein product
StatusApproved
AliasesK23, DKFZP434G032, HAIK1, CK23, MGC26158
Ensembl geneENSG00000108244
Ensembl biotypeprotein_coding
OMIM606194
Entrez25984

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 4 protein_coding, 2 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000209718, ENST00000436344, ENST00000462312, ENST00000485751, ENST00000494691, ENST00000582283, ENST00000582754, ENST00000584517, ENST00000585006

RefSeq mRNA: 2 — MANE Select: NM_015515 NM_001282433, NM_015515

CCDS: CCDS11380, CCDS62182

Canonical transcript exons

ENST00000209718 — 9 exons

ExonStartEnd
ENSE000008634524093620840936953
ENSE000018446684093734640937646
ENSE000035176754092270040923083
ENSE000035200654092994040930096
ENSE000035242804092447240924503
ENSE000035537344092844640928607
ENSE000036014804093137340931455
ENSE000036605934092823840928360
ENSE000036688054092535440925574

Expression profiles

Bgee: expression breadth ubiquitous, 127 present calls, max score 98.42.

FANTOM5 (CAGE): breadth broad, TPM avg 4.7058 / max 478.9005, expressed in 408 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter IDTPM avgSamples expressed
1658444.5365400
1658470.053923
1658450.030110
1658460.02046
1658480.01803
1658490.01615
1658500.01194
1658520.00763
1658530.00763
1658510.00372

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
placentaUBERON:000198798.42gold quality
skin of legUBERON:000151197.85gold quality
zone of skinUBERON:000001497.79gold quality
skin of abdomenUBERON:000141697.71gold quality
olfactory segment of nasal mucosaUBERON:000538696.14gold quality
saliva-secreting glandUBERON:000104495.53gold quality
minor salivary glandUBERON:000183095.19gold quality
bloodUBERON:000017893.30gold quality
islet of LangerhansUBERON:000000690.26gold quality
tonsilUBERON:000237288.11gold quality
right uterine tubeUBERON:000130288.00gold quality
left testisUBERON:000453386.81gold quality
testisUBERON:000047386.77gold quality
right testisUBERON:000453484.52gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047384.50gold quality
prostate glandUBERON:000236784.40gold quality
gall bladderUBERON:000211081.39gold quality
lower esophagus mucosaUBERON:003583480.71gold quality
pancreasUBERON:000126474.17gold quality
esophagus mucosaUBERON:000246974.05gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099173.41gold quality
thoracic mammary glandUBERON:000520073.08gold quality
fallopian tubeUBERON:000388972.77gold quality
granulocyteCL:000009470.50gold quality
leukocyteCL:000073869.83gold quality
endometriumUBERON:000129569.28gold quality
vermiform appendixUBERON:000115468.80gold quality
monocyteCL:000057668.62gold quality
vaginaUBERON:000099668.42gold quality
urinary bladderUBERON:000125567.82gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-HCAD-1yes13.30
E-MTAB-8060no636.76
E-GEOD-124858no33.48
E-CURD-10no23.90
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

31 targeting KRT23, 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-1468-3P99.9672.743797
HSA-MIR-454-3P99.9174.011925
HSA-MIR-130A-3P99.9073.311861
HSA-MIR-130B-3P99.9073.271850
HSA-MIR-301A-3P99.9073.151839
HSA-MIR-301B-3P99.9073.191836
HSA-MIR-366699.9073.241833
HSA-MIR-429599.9073.111838
HSA-MIR-106A-5P99.9073.942683
HSA-MIR-17-5P99.8973.832665
HSA-MIR-106B-5P99.8874.722795
HSA-MIR-20A-5P99.8874.762769
HSA-MIR-20B-5P99.8874.012621
HSA-MIR-519D-3P99.8873.972607
HSA-MIR-526B-3P99.8874.062587
HSA-MIR-93-5P99.8873.982606
HSA-MIR-797899.8666.90856
HSA-MIR-128399.6972.423009
HSA-MIR-519A-3P99.6771.671868
HSA-MIR-519B-3P99.6771.671868
HSA-MIR-519C-3P99.6771.671870
HSA-MIR-127599.4767.902749
HSA-MIR-806599.1970.381289
HSA-MIR-625-5P99.0268.642031
HSA-MIR-429998.2866.96850
HSA-MIR-4665-5P97.9167.691536
HSA-MIR-873-3P96.8466.09786
HSA-MIR-3189-3P96.8066.34896
HSA-MIR-7848-3P95.6965.00363
HSA-MIR-4732-5P90.0764.77412

Literature-anchored findings (GeneRIF, showing 9)

  • Keratin23 expression is a novel and important difference between microsatellite-stable and microsatellite-instable colon cancers. (PMID:19383294)
  • Data suggest a regulatory circuitry involving Smad4 dependent up-regulation of KRT23 (directly or indirectly) which in turn modulates the interaction between KRT23 and 14-3-3epsilon leading to a cytoplasmic sequestration of 14-3-3epsilon. (PMID:21492476)
  • Increased expression of KRT23 is associated with colorectal cancer. (PMID:23682078)
  • Data show that Keratin23 (KRT23) knockdown affected molecules of the cell cycle and DNA replication, recombination and repair. (PMID:24039993)
  • transcriptome studies identified keratin 23 as a new ductular cell marker in patients with alcoholic hepatitis (PMID:27752144)
  • highly elevated in hepatocellular carcinoma (PMID:30697791)
  • AUthors investigated KRT23 mRNA levels in datasets from liver biopsies of chronic hepatitis C (CHC) patients and in primary human hepatocytes experimentally infected with HCV, in addition to hepatoma cells. In each of these specimens, we observed an HCV-dependent increase of mRNA levels. Importantly, the KRT23 protein levels in patient plasma decreased upon viral clearance. (PMID:31216713)
  • The Overexpression of Keratin 23 Promotes Migration of Ovarian Cancer via Epithelial-Mesenchymal Transition. (PMID:33204716)
  • Immune checkpoint gene signature assesses immune infiltration profiles in bladder cancer and identifies KRT23 as an immunotherapeutic target. (PMID:39160525)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusKrt23ENSMUSG00000006777
rattus_norvegicusKrt23ENSRNOG00000011907

Paralogs (68): KRT33A (ENSG00000006059), VIM (ENSG00000026025), KRT31 (ENSG00000094796), NEFM (ENSG00000104722), 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), KRT6C (ENSG00000170465), KRT4 (ENSG00000170477), KRT74 (ENSG00000170484), KRT72 (ENSG00000170486), KRT83 (ENSG00000170523), BFSP2 (ENSG00000170819), KRT19 (ENSG00000171345), KRT15 (ENSG00000171346), KRT38 (ENSG00000171360), KRT13 (ENSG00000171401)

Protein

Protein identifiers

Keratin, type I cytoskeletal 23 — Q9C075 (reviewed: Q9C075)

Alternative names: Cytokeratin-23, Keratin-23

All UniProt accessions (4): Q9C075, J3QR55, K7EPI0, Q9UFN7

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Heterotetramer of two type I and two type II keratins.

Miscellaneous. There are two types of cytoskeletal and microfibrillar keratin: I (acidic; 40-55 kDa) and II (neutral to basic; 56-70 kDa).

Similarity. Belongs to the intermediate filament family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9C075-11yes
Q9C075-22

RefSeq proteins (2): NP_001269362, NP_056330* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002957Keratin_IFamily
IPR018039IF_conservedConserved_site
IPR039008IF_rod_domDomain

Pfam: PF00038

UniProt features (18 total): region of interest 8, sequence conflict 4, sequence variant 2, chain 1, domain 1, compositionally biased region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9C075-F178.510.50

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-6805567Keratinization
R-HSA-6809371Formation of the cornified envelope
R-HSA-9925563Developmental Lineage of Pancreatic Ductal Cells
R-HSA-1266738Developmental Biology

MSigDB gene sets: 155 (showing top): GOBP_MORPHOGENESIS_OF_AN_EPITHELIUM, GOBP_EPITHELIUM_DEVELOPMENT, GOBP_INTERMEDIATE_FILAMENT_BASED_PROCESS, GOBP_INTERMEDIATE_FILAMENT_ORGANIZATION, JAEGER_METASTASIS_DN, LHX3_01, TTGCWCAAY_CEBPB_02, TCF4_Q5, CEBP_Q2, KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP, MARTINEZ_RB1_TARGETS_DN, GATA6_01, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP, LIAO_METASTASIS, TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_DUCTAL_NORMAL_DN

GO Biological Process (3): morphogenesis of an epithelium (GO:0002009), epithelial cell differentiation (GO:0030855), intermediate filament organization (GO:0045109)

GO Molecular Function (3): structural constituent of skin epidermis (GO:0030280), structural molecule activity (GO:0005198), protein binding (GO:0005515)

GO Cellular Component (4): cytosol (GO:0005829), cytoskeleton (GO:0005856), keratin filament (GO:0045095), intermediate filament (GO:0005882)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Developmental Biology1
Keratinization1
Developmental Cell Lineages of the Exocrine Pancreas1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
epithelium development2
tissue morphogenesis1
cell differentiation1
intermediate filament cytoskeleton organization1
supramolecular fiber organization1
structural molecule activity1
molecular_function1
binding1
cytoplasm1
cellular anatomical structure1
intracellular membraneless organelle1
intermediate filament1
intermediate filament cytoskeleton1
polymeric cytoskeletal fiber1

Protein interactions and networks

STRING

584 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
KRT23CDKN3Q16667549
KRT23CDC26Q8NHZ8462
KRT23ANAPC7Q9UJX3461
KRT23ANAPC4Q9UJX5455
KRT23ANAPC1Q9H1A4437
KRT23ANAPC11Q9NYG5437
KRT23AHSGP02765407
KRT23S100A8P05109406
KRT23CDKN1AP38936387
KRT23MREGQ8N565387
KRT23DPP4P27487380
KRT23RASL10BQ96S79380
KRT23VAT1LQ9HCJ6375
KRT23SH2D7A6NKC9372
KRT23PRSS53Q2L4Q9371

IntAct

9 interactions, top by confidence:

ABTypeScore
CFTRESYT2psi-mi:“MI:0914”(association)0.710
RUNX1T1KRT23psi-mi:“MI:0915”(physical association)0.560
E6CASKpsi-mi:“MI:0914”(association)0.520
KRT23SNAPINpsi-mi:“MI:0914”(association)0.350
KRT23NESpsi-mi:“MI:0914”(association)0.350
RUNX1T1KRT23psi-mi:“MI:0915”(physical association)0.000
KRT23APCpsi-mi:“MI:0915”(physical association)0.000

BioGRID (32): KRT23 (Affinity Capture-MS), KRT23 (Affinity Capture-MS), KRT23 (Affinity Capture-MS), KRT23 (Affinity Capture-MS), KRT23 (Two-hybrid), SNAPIN (Affinity Capture-MS), HAUS4 (Affinity Capture-MS), GRIPAP1 (Affinity Capture-MS), NEFL (Affinity Capture-MS), TRAF7 (Affinity Capture-MS), HAUS3 (Affinity Capture-MS), ATG16L1 (Affinity Capture-MS), HAUS1 (Affinity Capture-MS), INA (Affinity Capture-MS), EPPK1 (Affinity Capture-MS)

ESM2 similar proteins: A0JND2, A3KN27, A6BLY7, A6H712, A6QNX5, A6QQJ3, A7YWK3, D3ZER2, E1AB55, O76014, O76015, P08552, P15331, P21807, P35617, P41219, P46660, P48670, Q0VBK2, Q13515, Q148H5, Q148H6, Q148H8, Q14CN4, Q28177, Q3SY84, Q3TRJ4, Q6A162, Q6IFW3, Q6IFW8, Q6IFX0, Q6IFX4, Q6IFZ9, Q6IG04, Q6IME9, Q6IMF1, Q6KB66, Q6NVD9, Q6NXH9, Q7RTS7

Diamond homologs: A1L595, A5A6M0, A5A6M5, A5A6P3, A6BLY7, A6QQJ3, A6QQQ9, A7YWM2, B0LKP1, B1AQ75, O18740, O57607, O57611, O76009, O76011, O76013, O76014, O76015, O77727, O93256, P02533, P02534, P02535, P02537, P05783, P05784, P05785, P06394, P08727, P08728, P08730, P08777, P08778, P08779, P13645, P13646, P15331, P19012, P21807, P23239

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance61
Likely benign6
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

847 predictions. Top by Δscore:

VariantEffectΔscore
17:40925349:CTT:Cdonor_loss1.0000
17:40925351:T:TGdonor_loss1.0000
17:40925352:A:ACdonor_gain1.0000
17:40925352:AC:Adonor_gain1.0000
17:40925353:C:CCdonor_gain1.0000
17:40925353:CC:Cdonor_gain1.0000
17:40925353:CCCTT:Cdonor_gain1.0000
17:40925570:GATTT:Gacceptor_gain1.0000
17:40925571:ATTT:Aacceptor_gain1.0000
17:40925572:TTT:Tacceptor_gain1.0000
17:40925573:TT:Tacceptor_gain1.0000
17:40925574:TC:Tacceptor_loss1.0000
17:40925575:C:Aacceptor_loss1.0000
17:40925575:C:CCacceptor_gain1.0000
17:40928233:CTCA:Cdonor_loss1.0000
17:40928234:TCA:Tdonor_loss1.0000
17:40928235:CAC:Cdonor_loss1.0000
17:40928236:ACC:Adonor_loss1.0000
17:40928237:CCGTG:Cdonor_gain1.0000
17:40928357:CAGA:Cacceptor_gain1.0000
17:40928359:GA:Gacceptor_gain1.0000
17:40928361:C:CCacceptor_gain1.0000
17:40928370:C:CTacceptor_gain1.0000
17:40928443:TA:Tdonor_loss1.0000
17:40928444:ACCT:Adonor_loss1.0000
17:40928445:C:CAdonor_loss1.0000
17:40928604:TTTC:Tacceptor_gain1.0000
17:40928605:TTC:Tacceptor_gain1.0000
17:40928606:TC:Tacceptor_gain1.0000
17:40928607:CC:Cacceptor_gain1.0000

AlphaMissense

2799 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:40931404:C:GA150P0.984
17:40936359:C:GR82P0.983
17:40928257:A:GL301P0.981
17:40930022:A:GL185P0.978
17:40925413:T:AK361N0.976
17:40925413:T:GK361N0.976
17:40930040:C:GR179P0.975
17:40936293:A:GI104T0.975
17:40925381:C:GR372P0.974
17:40936318:C:GA96P0.972
17:40925405:A:GL364P0.971
17:40925477:A:GL340P0.970
17:40929968:A:GL203P0.970
17:40930001:A:GL192P0.969
17:40925393:A:GI368T0.967
17:40925375:A:GL374P0.964
17:40925414:T:AK361I0.962
17:40925426:A:GL357P0.961
17:40936368:A:GL79P0.960
17:40930043:A:GL178P0.954
17:40936356:A:GL83P0.954
17:40936365:T:AN80I0.953
17:40931395:C:GA153P0.952
17:40925465:C:GR344P0.951
17:40929997:T:AE193D0.951
17:40929997:T:GE193D0.951
17:40925393:A:CI368S0.950
17:40925468:A:GL343P0.950
17:40936218:A:GL129P0.950
17:40936344:A:GL87P0.949

dbSNP variants (sampled 300 via entrez): RS1000453958 (17:40934091 T>C), RS1001074484 (17:40937813 G>T), RS1001147641 (17:40923306 G>C), RS1001166156 (17:40931223 G>T), RS1001452066 (17:40924811 T>C), RS1001480765 (17:40926601 T>C), RS1001534998 (17:40931141 A>G), RS1001536294 (17:40926859 G>A), RS1001794063 (17:40937717 C>A,T), RS1001923664 (17:40928120 A>G), RS1002733542 (17:40938269 A>G), RS1002821586 (17:40937028 A>G), RS1002910185 (17:40932528 G>A), RS1002962609 (17:40932162 G>A), RS1003054577 (17:40934367 C>T)

Disease associations

OMIM: gene MIM:606194 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

StudyTraitp-value
GCST000522_4Height8.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

64 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Estradiolincreases expression, decreases expression, affects cotreatment7
Valproic Acidaffects cotreatment, increases expression, affects expression, increases methylation7
Benzo(a)pyreneaffects methylation, decreases expression, increases expression6
Particulate Matterincreases expression, affects cotreatment, increases abundance5
Tetrachlorodibenzodioxinaffects cotreatment, decreases expression, increases expression4
Cyclosporinedecreases expression, increases expression4
Aflatoxin B1affects expression, increases expression4
Air Pollutantsincreases abundance, increases expression, decreases expression3
Ethinyl Estradiolaffects expression, decreases expression3
Progesteroneaffects cotreatment, decreases expression3
sodium arsenitedecreases expression, increases expression2
Smokedecreases expression, increases abundance2
Tobacco Smoke Pollutionaffects expression, increases expression2
Copper Sulfatedecreases expression, increases expression2
Genisteinaffects expression, decreases expression2
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
propionaldehydeincreases expression1
bisphenol Aaffects expression1
pyrogallol 1,3-dimethyl etherincreases expression, affects cotreatment, decreases expression, affects localization1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
butyraldehydeincreases expression1
benzo(e)pyreneincreases methylation1
hydroquinoneincreases expression1
pentanalincreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608increases reaction, affects binding1
entinostatincreases expression1
K 7174increases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 75

This page pulls from 75 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomereactomeparentrefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot