KRT78

gene
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Also known as K5B

Summary

KRT78 (keratin 78, HGNC:28926) is a protein-coding gene on chromosome 12q13.13, encoding Keratin, type II cytoskeletal 78 (Q8N1N4).

This gene is a member of the type II keratin gene family and encodes a protein with an intermediate filament domain. Keratins are the major structural proteins in epithelial cells, forming a cytoplasmic network of 10 to 12 nm wide intermediate filaments and creating a scaffold that gives cells the ability to withstand mechanical and non-mechanical stresses. The genes of the type II keratin family are located as a gene cluster at 12p13.13. Four pseudogenes of this gene family have been identified.

Source: NCBI Gene 196374 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 117 total
  • MANE Select transcript: NM_173352

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28926
Approved symbolKRT78
Namekeratin 78
Location12q13.13
Locus typegene with protein product
StatusApproved
AliasesK5B
Ensembl geneENSG00000170423
Ensembl biotypeprotein_coding
OMIM611159
Entrez196374

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000304620, ENST00000359499, ENST00000547110, ENST00000547920, ENST00000551581

RefSeq mRNA: 2 — MANE Select: NM_173352 NM_001300814, NM_173352

CCDS: CCDS73473, CCDS8840

Canonical transcript exons

ENST00000304620 — 9 exons

ExonStartEnd
ENSE000011530725283945352839487
ENSE000012661585284854752848994
ENSE000012981235284409352844218
ENSE000013128725283780752839372
ENSE000016590055283976452839984
ENSE000017997705284455952844723
ENSE000035531935284790752848121
ENSE000036434785284676452846824
ENSE000036848405284619752846292

Expression profiles

Bgee: expression breadth ubiquitous, 154 present calls, max score 99.88.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.5914 / max 662.1607, expressed in 51 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
1311681.490444
1311700.043713
1311660.020010
1311690.01907
1311670.01008
1311650.00833

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
lower esophagus mucosaUBERON:003583499.88gold quality
buccal mucosa cellCL:000233699.48gold quality
oral cavityUBERON:000016798.75gold quality
esophagus squamous epitheliumUBERON:000692098.45gold quality
pharyngeal mucosaUBERON:000035598.44gold quality
amniotic fluidUBERON:000017397.94gold quality
esophagus mucosaUBERON:000246997.85gold quality
skin of legUBERON:000151196.01gold quality
body of tongueUBERON:001187695.22gold quality
gingivaUBERON:000182895.12gold quality
skin of abdomenUBERON:000141694.64gold quality
gingival epitheliumUBERON:000194993.87gold quality
zone of skinUBERON:000001493.69gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047391.30gold quality
tongueUBERON:000172390.89gold quality
superior surface of tongueUBERON:000737186.48gold quality
penisUBERON:000098986.04gold quality
mammalian vulvaUBERON:000099784.12gold quality
vaginaUBERON:000099682.89gold quality
upper leg skinUBERON:000426282.23gold quality
tonsilUBERON:000237281.29gold quality
esophagusUBERON:000104380.55gold quality
skin of hipUBERON:000155478.78gold quality
nippleUBERON:000203078.65gold quality
epithelium of nasopharynxUBERON:000195178.33gold quality
palpebral conjunctivaUBERON:000181275.55gold quality
spermCL:000001973.40gold quality
ectocervixUBERON:001224970.83gold quality
mouth mucosaUBERON:000372969.79gold quality
eyeUBERON:000097068.07gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-MTAB-8221yes8579.13
E-ANND-3no2.70

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

62 targeting KRT78, 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-126-5P100.0072.713180
HSA-MIR-432-3P100.0067.86705
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-12118100.0065.881270
HSA-MIR-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-4692100.0067.322066
HSA-MIR-4713-3P100.0065.92505
HSA-MIR-450099.9972.722367
HSA-MIR-451499.9967.101870
HSA-MIR-3173-3P99.9866.491217
HSA-MIR-6891-5P99.9866.531372
HSA-LET-7A-5P99.9872.291790
HSA-LET-7B-5P99.9872.311790
HSA-LET-7C-5P99.9872.291790
HSA-LET-7E-5P99.9872.291790
HSA-LET-7F-5P99.9872.561784
HSA-LET-7G-5P99.9872.371784
HSA-LET-7I-5P99.9872.371788
HSA-MIR-98-5P99.9872.331787
HSA-MIR-445899.9671.641650
HSA-MIR-589-3P99.9169.622088
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-449299.8768.253611
HSA-MIR-1211999.8768.351653
HSA-MIR-62399.7668.161170
HSA-MIR-442899.7366.411733
HSA-MIR-6512-3P99.6566.071468
HSA-MIR-6720-5P99.6566.221459
HSA-MIR-449899.4767.422360

Literature-anchored findings (GeneRIF, showing 1)

  • K78 is strongly expressed in the basal and parabasal cell layers with decreasing intensity in the lower suprabasal cells of keratinising and non-keratinising squamous epithelia and keratinocyte cultures. (PMID:26340985)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusKrt78ENSMUSG00000050463
rattus_norvegicusKrt78ENSRNOG00000059790

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), 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 II cytoskeletal 78Q8N1N4 (reviewed: Q8N1N4)

Alternative names: Cytokeratin-78, Keratin-5b, Keratin-78, Type-II keratin Kb40

All UniProt accessions (2): Q8N1N4, H0YI54

UniProt curated annotations — full annotation on UniProt →

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

Tissue specificity. In non-keratinising esophageal and vaginal epithelium, strongly expressed in the basal and parabasal/lower suprabasal cell layers with considerably decreased expression in the mid/upper suprabasal layers (at protein level). A similar gradient from basal to lower suprabasal layers is seen in the partially keratinised dorsal tongue epithelium, in the scalp and in the plantar epidermis (at protein level). Extension of expression into the suprabasal compartments is distinctly more pronounced in non-keratinising epithelia than in keratinising epithelia and epidermis (at protein level). In scalp sections, present in the interfollicular epidermis and infundibulum including the entire outer root sheath of the hair follicles and also in the sebocytes (at protein level). In sweat glands, expressed in peripheral and luminal cells of the lower duct and in peripheral cells of the middle/upper duct with no expression observed in luminal cells (at protein level). In embryos at the 14th week of pregnancy, detected in basal and parabasal layers but is absent from the uppermost epidermal layer (at protein level). Expressed in tongue epithelium.

Miscellaneous. 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.

Isoforms (2)

UniProt IDNamesCanonical?
Q8N1N4-11yes
Q8N1N4-22

RefSeq proteins (2): NP_001287743, NP_775487* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003054Keratin_IIFamily
IPR018039IF_conservedConserved_site
IPR032444Keratin_2_headDomain
IPR039008IF_rod_domDomain

Pfam: PF00038, PF16208

UniProt features (18 total): region of interest 7, sequence variant 4, splice variant 2, sequence conflict 2, chain 1, domain 1, site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N1N4-F171.930.48

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): 362 (stutter)

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

IDPathway
R-HSA-6805567Keratinization
R-HSA-6809371Formation of the cornified envelope
R-HSA-9725554Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin
R-HSA-1266738Developmental Biology
R-HSA-9734767Developmental Cell Lineages

MSigDB gene sets: 64 (showing top): GOBP_EPITHELIUM_DEVELOPMENT, GOBP_INTERMEDIATE_FILAMENT_BASED_PROCESS, GOBP_INTERMEDIATE_FILAMENT_ORGANIZATION, GOBP_EPIDERMAL_CELL_DIFFERENTIATION, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP, TGANTCA_AP1_C, GOBP_EPIDERMIS_DEVELOPMENT, GOBP_KERATINIZATION, GOBP_SKIN_DEVELOPMENT, CP2_01, GOCC_INTERMEDIATE_FILAMENT_CYTOSKELETON, GOCC_KERATIN_FILAMENT, DODD_NASOPHARYNGEAL_CARCINOMA_DN, GOMF_STRUCTURAL_MOLECULE_ACTIVITY, LIN_SILENCED_BY_TUMOR_MICROENVIRONMENT

GO Biological Process (2): keratinization (GO:0031424), intermediate filament organization (GO:0045109)

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

GO Cellular Component (5): obsolete extracellular space (GO:0005615), cytosol (GO:0005829), keratin filament (GO:0045095), extracellular exosome (GO:0070062), intermediate filament (GO:0005882)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Developmental Biology2
Keratinization1
Developmental Cell Lineages of the Integumentary System1

GO top-level categories

Rollup of top GO terms by namespace:

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

Protein interactions and networks

STRING

1011 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
KRT78PDPNQ86YL7476
KRT78CYSRT1A8MQ03449
KRT78RRM1P23921441
KRT78POLEQ07864441
KRT78TYMSP04818439
KRT78KRT72Q14CN4426
KRT78C20orf204A0A1B0GTL2399
KRT78SMIM5Q71RC9396
KRT78CRNNQ9UBG3388
KRT78NDUFV2P19404381
KRT78PRMT1Q99873371
KRT78SPRR2EP22531370
KRT78SPRR3Q9UBC9370
KRT78SCELO95171358
KRT78KRTAP3-1Q9BYR8351

IntAct

81 interactions, top by confidence:

ABTypeScore
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
KRT33BKRT78psi-mi:“MI:0915”(physical association)0.630
KRT78KRT35psi-mi:“MI:0915”(physical association)0.630
YWHAHBLTP3Bpsi-mi:“MI:0914”(association)0.570
KRT27KRT78psi-mi:“MI:0915”(physical association)0.560
KRT36KRT78psi-mi:“MI:0915”(physical association)0.560
KRT31KRT78psi-mi:“MI:0915”(physical association)0.560
KRT25KRT78psi-mi:“MI:0915”(physical association)0.560
KRT15KRT78psi-mi:“MI:0915”(physical association)0.560
KRT78TRIM54psi-mi:“MI:0915”(physical association)0.560
KRT14KRT78psi-mi:“MI:0915”(physical association)0.560
KRT19KRT78psi-mi:“MI:0915”(physical association)0.560
KRT16KRT78psi-mi:“MI:0915”(physical association)0.560
KRT34KRT78psi-mi:“MI:0915”(physical association)0.560
KRT39KRT78psi-mi:“MI:0915”(physical association)0.560
KRT78C14orf119psi-mi:“MI:0915”(physical association)0.560
PPP2R2BDDX3Xpsi-mi:“MI:0914”(association)0.460
ABL1psi-mi:“MI:0914”(association)0.350
WTAPDDX39Apsi-mi:“MI:0914”(association)0.350
METTL14HMGB1P1psi-mi:“MI:0914”(association)0.350
COPS5FBLL1psi-mi:“MI:0914”(association)0.350
CUL2ANXA2P2psi-mi:“MI:0914”(association)0.350
CUL3PXDNLpsi-mi:“MI:0914”(association)0.350
LRRK2psi-mi:“MI:0914”(association)0.350

BioGRID (102): KRT78 (Affinity Capture-MS), KRT78 (Affinity Capture-MS), KRT78 (Biochemical Activity), KRT78 (Affinity Capture-MS), KRT78 (Affinity Capture-MS), KRT78 (Affinity Capture-MS), KRT78 (Affinity Capture-MS), KRT78 (Affinity Capture-MS), KRT78 (Affinity Capture-MS), KRT78 (Affinity Capture-MS), KRT78 (Affinity Capture-MS), KRT78 (Affinity Capture-MS), KRT78 (Affinity Capture-MS), KRT78 (Affinity Capture-MS), KRT78 (Two-hybrid)

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: A0A8C0N8E3, A0JND2, A3KN27, A4FUZ0, A5A6M6, A5A6M8, A5A6N0, A6QNX5, A6QQJ3, A7YWK3, E1AB55, O43790, O93532, O95678, P02538, P04104, P04259, P04264, P04265, P04266, P05786, P05787, P07744, P08670, P08729, P08776, P11679, P12035, P13647, P15241, P15331, P16878, P18520, P19013, P21807, P25691, P35908, P41219, P48616, P48668

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 61 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 envelope1226.4×4e-12
Keratinization1216.7×4e-10

GO biological processes:

GO termPartnersFoldFDR
morphogenesis of an epithelium1279.4×9e-18
intermediate filament organization1255.6×5e-16
epithelial cell differentiation1033.8×5e-11
autophagy510.6×8e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance91
Likely benign13
Benign7

Top pathogenic / likely-pathogenic (0)

SpliceAI

1273 predictions. Top by Δscore:

VariantEffectΔscore
12:52839758:CCTCA:Cdonor_loss1.0000
12:52839759:CTCA:Cdonor_loss1.0000
12:52839760:TCAC:Tdonor_loss1.0000
12:52839761:CAC:Cdonor_loss1.0000
12:52839762:A:ACdonor_gain1.0000
12:52839762:A:Cdonor_loss1.0000
12:52839763:C:CCdonor_gain1.0000
12:52839980:GCGTT:Gacceptor_gain1.0000
12:52839981:CGTT:Cacceptor_gain1.0000
12:52839981:CGTTC:Cacceptor_gain1.0000
12:52839983:TT:Tacceptor_gain1.0000
12:52839985:C:CCacceptor_gain1.0000
12:52839986:T:Aacceptor_loss1.0000
12:52839992:CGGGG:Cacceptor_gain1.0000
12:52839993:G:Tacceptor_gain1.0000
12:52839996:G:Cacceptor_gain1.0000
12:52839996:G:GCacceptor_gain1.0000
12:52844219:C:CCacceptor_gain1.0000
12:52844580:AG:Adonor_gain1.0000
12:52844581:G:Cdonor_gain1.0000
12:52844586:AG:Adonor_gain1.0000
12:52844719:AGCTC:Aacceptor_gain1.0000
12:52844721:CTC:Cacceptor_gain1.0000
12:52844722:TC:Tacceptor_gain1.0000
12:52844723:CC:Cacceptor_gain1.0000
12:52844723:CCTG:Cacceptor_loss1.0000
12:52844724:C:CCacceptor_gain1.0000
12:52844725:T:Cacceptor_loss1.0000
12:52846107:C:Adonor_gain1.0000
12:52846178:C:Adonor_gain1.0000

AlphaMissense

3396 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:52846767:C:AK219N0.953
12:52846767:C:GK219N0.953
12:52848565:A:CF122L0.949
12:52848565:A:TF122L0.949
12:52848567:A:GF122L0.949
12:52844582:C:GA300P0.930
12:52844124:A:GL339P0.919
12:52848566:A:GF122S0.879
12:52848587:A:GI115T0.877
12:52844145:A:GL332P0.874
12:52844208:A:GL311P0.865
12:52848566:A:CF122C0.864
12:52848895:G:CF12L0.864
12:52848895:G:TF12L0.864
12:52848897:A:GF12L0.864
12:52848102:T:GQ135P0.863
12:52848556:G:CF125L0.862
12:52848556:G:TF125L0.862
12:52848558:A:GF125L0.862
12:52846275:G:CF226L0.861
12:52846275:G:TF226L0.861
12:52846277:A:GF226L0.861
12:52846218:G:CF245L0.859
12:52846218:G:TF245L0.859
12:52846220:A:GF245L0.859
12:52844103:A:GL346P0.855
12:52839823:C:AK403N0.846
12:52839823:C:GK403N0.846
12:52846779:A:CF215L0.846
12:52846779:A:TF215L0.846

dbSNP variants (sampled 300 via entrez): RS1000796199 (12:52839704 G>A,C), RS1001068331 (12:52844126 C>T), RS1001113238 (12:52837746 G>A), RS1001373091 (12:52850118 C>A), RS1001397543 (12:52845490 C>T), RS1001732508 (12:52840441 G>A,T), RS1001741924 (12:52846714 T>G), RS1002025733 (12:52846535 G>A,C), RS1002070489 (12:52845305 C>T), RS1002173907 (12:52844957 C>T), RS1002299132 (12:52850962 G>A), RS1002520075 (12:52839267 C>A,T), RS1002555292 (12:52843611 A>T), RS1002624009 (12:52847776 G>A,T), RS1002912973 (12:52843918 C>T)

Disease associations

OMIM: gene MIM:611159 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST006019_37Gamma glutamyl transferase levels7.000000e-09
GCST90011899_17Aspartate aminotransferase levels2.000000e-10

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004532serum gamma-glutamyl transferase measurement
EFO:0004736aspartate aminotransferase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyrenedecreases expression, decreases methylation2
Tobacco Smoke Pollutionincreases expression2
aristolochic acid Iincreases expression1
sodium arsenatedecreases expression, increases abundance1
pyrogallol 1,3-dimethyl etheraffects cotreatment, affects localization, decreases expression, increases expression1
terbufosincreases methylation1
arseniteincreases methylation1
hydroquinoneincreases expression1
CGP 52608affects binding, increases reaction1
abrineincreases expression1
bisphenol Saffects expression1
Allergensincreases expression1
Arsenicdecreases expression, increases abundance1
Cadmiumaffects binding1
Diazinonincreases methylation1
Dinitrochlorobenzeneaffects binding1
Fonofosincreases methylation1
Furaldehydeaffects cotreatment, affects localization, decreases expression, increases expression1
Parathionincreases methylation1
Sodium Chlorideincreases expression, affects cotreatment, decreases expression, affects localization1
Tetrachlorodibenzodioxinincreases expression1
Aflatoxin B1increases methylation1
Antirheumatic Agentsdecreases expression1
Cadmium Chlorideincreases expression1
Okadaic Acidincreases expression1
beta-Naphthoflavoneincreases expression1
Lactic Aciddecreases expression1
Genisteinincreases reaction, affects binding1

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.