CRNN

gene
On this page

Also known as SEP53

Summary

CRNN (cornulin, HGNC:1230) is a protein-coding gene on chromosome 1q21.3, encoding Cornulin (Q9UBG3). Promotes cell proliferation, G1/S cell cycle progression and induces expression of the cell cycle regulator CCND1.

This gene encodes a member of the “fused gene” family of proteins, which contain N-terminus EF-hand domains and multiple tandem peptide repeats. The encoded protein contains two EF-hand Ca2+ binding domains in its N-terminus and two glutamine- and threonine-rich 60 amino acid repeats in its C-terminus. This gene, also known as squamous epithelial heat shock protein 53, may play a role in the mucosal/epithelial immune response and epidermal differentiation.

Source: NCBI Gene 49860 — RefSeq curated summary.

At a glance

  • GWAS associations: 9
  • Clinical variants (ClinVar): 85 total
  • MANE Select transcript: NM_016190

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1230
Approved symbolCRNN
Namecornulin
Location1q21.3
Locus typegene with protein product
StatusApproved
AliasesSEP53
Ensembl geneENSG00000143536
Ensembl biotypeprotein_coding
OMIM611312
Entrez49860

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000271835

RefSeq mRNA: 1 — MANE Select: NM_016190 NM_016190

CCDS: CCDS1010

Canonical transcript exons

ENST00000271835 — 3 exons

ExonStartEnd
ENSE00000960720152412096152412246
ENSE00001177324152409243152410943
ENSE00001826834152414214152414263

Expression profiles

Bgee: expression breadth ubiquitous, 157 present calls, max score 99.96.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 9.3022 / max 5484.6232, expressed in 45 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
145639.077044
145640.206315
145610.01164
145620.00743

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
lower esophagus mucosaUBERON:003583499.96gold quality
tongue squamous epitheliumUBERON:000691999.82gold quality
pharyngeal mucosaUBERON:000035599.73gold quality
buccal mucosa cellCL:000233699.64gold quality
gingivaUBERON:000182899.52gold quality
gingival epitheliumUBERON:000194999.43gold quality
body of tongueUBERON:001187699.32gold quality
esophagus mucosaUBERON:000246999.29gold quality
cervix squamous epitheliumUBERON:000692299.22gold quality
squamous epitheliumUBERON:000691499.09gold quality
oral cavityUBERON:000016799.00gold quality
esophagus squamous epitheliumUBERON:000692098.84gold quality
amniotic fluidUBERON:000017398.38gold quality
cervix epitheliumUBERON:000480198.29gold quality
epithelium of esophagusUBERON:000197697.91gold quality
tongueUBERON:000172396.11gold quality
superior surface of tongueUBERON:000737190.90gold quality
vaginaUBERON:000099688.78gold quality
esophagusUBERON:000104384.92gold quality
periodontal ligamentUBERON:000826683.81gold quality
mammalian vulvaUBERON:000099783.74gold quality
tonsilUBERON:000237282.04gold quality
uterine cervixUBERON:000000281.96gold quality
penisUBERON:000098981.74gold quality
ectocervixUBERON:001224977.41gold quality
mouth mucosaUBERON:000372975.55gold quality
oviduct epitheliumUBERON:000480475.02gold quality
skin of legUBERON:000151173.47gold quality
skin of abdomenUBERON:000141672.54gold quality
spermCL:000001971.98silver quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-HCAD-1yes9811.69
E-ANND-3yes11.34

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting CRNN, 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-6755-5P99.9565.59464
HSA-MIR-539-5P99.9370.302855
HSA-MIR-5004-5P99.6866.631294
HSA-MIR-4756-3P99.6266.301319
HSA-MIR-6740-3P99.4868.491392
HSA-MIR-1224-5P99.4865.59803
HSA-MIR-329-5P99.2768.111597
HSA-MIR-128699.0966.231046
HSA-MIR-5197-3P98.7167.051905
HSA-MIR-950098.6266.541845
HSA-MIR-6841-3P98.0866.54604
HSA-MIR-219B-5P97.9165.80531
HSA-MIR-4638-3P97.9065.75905
HSA-MIR-3187-3P97.3865.80904
HSA-MIR-124397.0765.44719
HSA-MIR-444897.0466.22752
HSA-MIR-365496.4366.55646
HSA-MIR-3675-5P95.9065.80474

Literature-anchored findings (GeneRIF, showing 11)

  • SEP53 may be a component of the mucosal/epithelial innate immune response engaged in an ongoing interaction with a pathogen (PMID:17925851)
  • Results describe the cloning of porcine SEP53, its homology to the human protein, and its expression in the esophagus and in gastric squamous epithelium. (PMID:18465210)
  • CRNN mRNA expression is decreased in eczematous skin (PMID:19133922)
  • Negative regulation of SIRT1 by DBC1 may retard tumorigenesis in breast tissue, so the correlation between SIRT1 and DBC1 is a potential prognostic indicator in breast cancer. (PMID:20412117)
  • cornulin is an important molecule in normal esophageal pathology and is likely lost during the conversion of normal to neoplastic epithelium (PMID:22560086)
  • Findings demonstrate that CRNN is a tumor suppressor gene that plays a critical tumor suppressive role in ESCC. (PMID:23894350)
  • Loss of CRNN expression correlated with advanced tumor length, greater tumor invasion depth, lymph node metastasis, and poor survival in patients with esophageal squamous cell carcinoma. (PMID:24263008)
  • This study showed a significant correlation between LOH/MSI at 1q21.3 with clinical outcomes and that downregulation of CRNN gene could be considered as a prognostic marker of OSCC. (PMID:25846277)
  • The single-nucleotide polymorphisms of CRNN (rs941934) and RPTN (rs3001978, rs28441202) may contribute to Atopic Dermatitis development, but further studies on a larger group of Atopic Dermatitis patients are needed to verify this assumption. (PMID:28219068)
  • knockdown of CRNN by small interfering RNA suppressed G1/S transition and attenuated the M5-induced proliferation. In addition, CRNN overexpression increased the phosphorylation and activation of phosphoinositide 3-kinase and Akt. Inactivation of the phosphoinositide 3-kinase and Akt pathways using small interfering RNA or selective inhibitors (LY294002 and MK2206) reduced the proliferative effects of CRNN (PMID:30009832)
  • Identification of Down-Expressed CRNN Associated with Cancer Progression and Poor Prognosis in Laryngeal Squamous Cell Carcinoma. (PMID:38538265)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerios100sENSDARG00000036773
danio_rerios100a10aENSDARG00000037425
danio_rerios100tENSDARG00000055589
mus_musculusCrnnENSMUSG00000078657
rattus_norvegicusCrnnENSRNOG00000008721

Paralogs (21): S100A8 (ENSG00000143546), S100A7 (ENSG00000143556), S100B (ENSG00000160307), S100A1 (ENSG00000160678), S100A11 (ENSG00000163191), S100A9 (ENSG00000163220), S100A12 (ENSG00000163221), S100P (ENSG00000163993), S100G (ENSG00000169906), S100Z (ENSG00000171643), S100A7A (ENSG00000184330), S100A3 (ENSG00000188015), S100A16 (ENSG00000188643), SNTN (ENSG00000188817), S100A13 (ENSG00000189171), S100A14 (ENSG00000189334), S100A4 (ENSG00000196154), S100A5 (ENSG00000196420), S100A2 (ENSG00000196754), S100A10 (ENSG00000197747), S100A6 (ENSG00000197956)

Protein

Protein identifiers

CornulinQ9UBG3 (reviewed: Q9UBG3)

Alternative names: 53 kDa putative calcium-binding protein, 53 kDa squamous epithelial-induced stress protein, 58 kDa heat shock protein, Squamous epithelial heat shock protein 53, Tumor-related protein

All UniProt accessions (1): Q9UBG3

UniProt curated annotations — full annotation on UniProt →

Function. Promotes cell proliferation, G1/S cell cycle progression and induces expression of the cell cycle regulator CCND1. Regulates proliferation induced by pro-inflammatory cytokine response via activation of NFKB1 and PI3K/AKT signaling pathways.

Subunit / interactions. Homodimer.

Subcellular location. Cytoplasm.

Tissue specificity. Expressed in the basal skin layer (at protein level). Squamous epithelia cell-specific. Expressed in the esophagus (periphery of the cells of the granular and the upper spinous layers), foreskin (granular and lower cornified cells), scalp skin (granular layer), inner root sheath of the hair follicle and in primary keratinocytes (at protein level). Expressed in the squamous epithelium of the cervix, esophagus, foreskin and larynx. Expressed in the fetal bladder and scalp skin. Expressed at very low levels in the lung, kidney, uterus, skeletal muscle, heart and fetal brain. Undetectable or barely detectable in esophageal and oral squamous cell carcinoma compared with the matched adjacent normal esophageal mucosa. Undetectable or barely detectable in larynx and esophagus from patients with pH-documented laryngopharyngeal reflux (LPR).

Disease relevance. Esophageal cancer (ESCR) [MIM:133239] A malignancy of the esophagus. The most common types are esophageal squamous cell carcinoma and adenocarcinoma. Cancer of the esophagus remains a devastating disease because it is usually not detected until it has progressed to an advanced incurable stage. Disease susceptibility is associated with variants affecting the gene represented in this entry. CRNN expression is increased in psoriasis patients suggesting a potential role in disease pathogenesis.

Domain organisation. The EF-hand is necessary for the colony survival activity to protect cells from death induced by exposure to DCA.

Induction. Up-regulated after heat shock, ponasterone A and deoxycholic acid. Induced in response to pro-inflammatory cytokines.

Similarity. Belongs to the S100-fused protein family.

RefSeq proteins (1): NP_057274* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002048EF_hand_domDomain
IPR011992EF-hand-dom_pairHomologous_superfamily
IPR013787S100_Ca-bd_subDomain
IPR018247EF_Hand_1_Ca_BSBinding_site
IPR034325S-100_domDomain

Pfam: PF01023

UniProt features (24 total): compositionally biased region 12, binding site 5, sequence variant 3, region of interest 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UBG3-F149.450.14

Functional residue map

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

Ligand- & substrate-binding residues (5): 62; 64; 66; 68; 73

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 69 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_DN, GOBP_RESPONSE_TO_PEPTIDE, LFA1_Q6, GOBP_KERATINOCYTE_PROLIFERATION, GOBP_CELL_CYCLE_PHASE_TRANSITION, GOBP_CELL_CELL_ADHESION, GOBP_POSITIVE_REGULATION_OF_MOLECULAR_FUNCTION, GOBP_PHOSPHATIDYLINOSITOL_3_KINASE_PROTEIN_KINASE_B_SIGNAL_TRANSDUCTION, GOBP_REGULATION_OF_KERATINOCYTE_PROLIFERATION, GOBP_REGULATION_OF_CELL_CYCLE, GOBP_REGULATION_OF_CELL_CYCLE_G1_S_PHASE_TRANSITION, GOBP_POSITIVE_REGULATION_OF_CELL_CYCLE_PROCESS, GOBP_CELL_CYCLE_G1_S_PHASE_TRANSITION, TGANTCA_AP1_C, GOBP_RESPONSE_TO_ABIOTIC_STIMULUS

GO Biological Process (8): response to heat (GO:0009408), regulation of gene expression (GO:0010468), positive regulation of keratinocyte proliferation (GO:0010838), obsolete positive regulation of NF-kappaB transcription factor activity (GO:0051092), regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction (GO:0051896), cellular response to cytokine stimulus (GO:0071345), cell-cell adhesion (GO:0098609), positive regulation of cell cycle G1/S phase transition (GO:1902808)

GO Molecular Function (5): calcium ion binding (GO:0005509), transition metal ion binding (GO:0046914), calcium-dependent protein binding (GO:0048306), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (3): cytoplasm (GO:0005737), membrane (GO:0016020), extracellular exosome (GO:0070062)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
metal ion binding2
cellular anatomical structure2
response to stress1
response to temperature stimulus1
gene expression1
regulation of macromolecule biosynthetic process1
regulation of keratinocyte proliferation1
keratinocyte proliferation1
positive regulation of epithelial cell proliferation1
phosphatidylinositol 3-kinase/protein kinase B signal transduction1
regulation of intracellular signal transduction1
response to cytokine1
cell adhesion1
cell cycle G1/S phase transition1
positive regulation of cell cycle phase transition1
regulation of cell cycle G1/S phase transition1
calcium ion binding1
protein binding1
binding1
cation binding1
intracellular anatomical structure1
extracellular vesicle1

Protein interactions and networks

STRING

1244 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CRNNDEPP1Q9NTK1952
CRNNTGM3Q08188698
CRNNCRCT1Q9UGL9571
CRNNKRT4P19013521
CRNNKRTDAPP60985516
CRNNTCHHL1Q5QJ38512
CRNNLORICRINP23490506
CRNNSCELO95171481
CRNNKRT32Q14532479
CRNNTMPRSS11BQ86T26474
CRNNKPRPQ5T749471
CRNNFLGP20930466
CRNNSPINK5Q9NQ38464
CRNNSPRR3Q9UBC9464
CRNNDSG1Q02413453

IntAct

97 interactions, top by confidence:

ABTypeScore
NOP10DKC1psi-mi:“MI:0914”(association)0.890
STIP1CCDC117psi-mi:“MI:0914”(association)0.770
COMMD1VPS26Cpsi-mi:“MI:0914”(association)0.730
SNW1AQRpsi-mi:“MI:0914”(association)0.650
NSL1NDC80psi-mi:“MI:0914”(association)0.640
DCTN5DCTN6psi-mi:“MI:0914”(association)0.640
RAP1GDS1DIRAS1psi-mi:“MI:0914”(association)0.640
LMO4CRNNpsi-mi:“MI:0915”(physical association)0.560
FTH1A2ML1psi-mi:“MI:0914”(association)0.530
FRMD1A2ML1psi-mi:“MI:0914”(association)0.530
WDR59EPB41L2psi-mi:“MI:0914”(association)0.530
UCP2CST4psi-mi:“MI:0914”(association)0.530
C1orf162KIAA1143psi-mi:“MI:0914”(association)0.530
NRMZG16Bpsi-mi:“MI:0914”(association)0.530
GPN3POLR3Apsi-mi:“MI:0914”(association)0.530
KIR2DS2RHOBTB3psi-mi:“MI:0914”(association)0.530
NPBCST4psi-mi:“MI:0914”(association)0.530
SFTA2TBCEpsi-mi:“MI:0914”(association)0.530
CIMAP3PSMG3psi-mi:“MI:0914”(association)0.530
SCAMP2SCAMP3psi-mi:“MI:0914”(association)0.530
RAG2CRNNpsi-mi:“MI:0915”(physical association)0.400
SNX15CRNNpsi-mi:“MI:0915”(physical association)0.400
B3GNT5CRNNpsi-mi:“MI:0915”(physical association)0.400
NPBIL16psi-mi:“MI:0914”(association)0.350

BioGRID (102): CRNN (Affinity Capture-MS), CRNN (Affinity Capture-MS), CRNN (Affinity Capture-MS), CRNN (Affinity Capture-MS), CRNN (Affinity Capture-MS), CRNN (Affinity Capture-MS), CRNN (Affinity Capture-MS), CRNN (Affinity Capture-MS), CRNN (Synthetic Lethality), CRNN (Affinity Capture-MS), CRNN (Affinity Capture-MS), SSX2IP (Affinity Capture-MS), CRNN (Affinity Capture-MS), CRNN (Affinity Capture-MS), CRNN (Affinity Capture-MS)

ESM2 similar proteins: A2VE23, A6NDE4, A6NEQ0, B3A0P1, P02672, P02674, P04279, P04474, P05995, P07186, P0C7A4, P0C7A5, P0C7P1, P0DJD3, P0DJD4, P11088, P11596, P13428, P20930, P24516, P55704, Q02383, Q10124, Q15415, Q21127, Q23935, Q24669, Q2VIS4, Q4X212, Q54T37, Q5U7M7, Q5U7M8, Q5U7M9, Q5U7N0, Q5U7N1, Q5U7N3, Q5U7N4, Q6AYN3, Q6E0U4, Q6JHY2

Diamond homologs: A6QP92, P20930, P37709, P97347, Q07283, Q2VIS4, Q5D862, Q5QJ38, Q6XPR3, Q9D3P1, Q9UBG3, A7K6Y8, A7K6Y9, O77691, O77791, P02632, P02633, P02634, P02638, P02639, P04271, P04631, P05109, P05942, P05943, P05964, P06702, P06703, P07091, P14069, P22793, P23297, P24479, P24480, P25815, P27004, P27005, P28318, P28782, P28783

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance75
Likely benign8
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

213 predictions. Top by Δscore:

VariantEffectΔscore
1:152410941:TTT:Tacceptor_gain1.0000
1:152410942:TT:Tacceptor_gain1.0000
1:152410942:TTCTG:Tacceptor_loss1.0000
1:152410943:TC:Tacceptor_loss1.0000
1:152410944:C:CAacceptor_loss1.0000
1:152410944:C:CCacceptor_gain1.0000
1:152410945:T:Gacceptor_loss1.0000
1:152412247:C:CCacceptor_gain1.0000
1:152410864:T:TAdonor_gain0.9900
1:152410939:GGTTT:Gacceptor_gain0.9900
1:152410940:GTTT:Gacceptor_gain0.9900
1:152412092:GTA:Gdonor_loss0.9900
1:152412093:TA:Tdonor_loss0.9900
1:152412095:CCA:Cdonor_gain0.9900
1:152412141:C:Adonor_gain0.9900
1:152412242:TCAAC:Tacceptor_gain0.9900
1:152412243:CAAC:Cacceptor_gain0.9900
1:152412243:CAACC:Cacceptor_gain0.9900
1:152412244:AAC:Aacceptor_gain0.9900
1:152412245:AC:Aacceptor_gain0.9900
1:152412245:ACC:Aacceptor_loss0.9900
1:152412246:CC:Cacceptor_gain0.9900
1:152412246:CCTG:Cacceptor_loss0.9900
1:152411080:AATTG:Adonor_gain0.9700
1:152412094:A:ACdonor_gain0.9700
1:152412095:C:CCdonor_gain0.9700
1:152414209:CTTA:Cdonor_loss0.9700
1:152414210:TTACC:Tdonor_loss0.9700
1:152414211:TA:Tdonor_loss0.9700
1:152412055:T:Adonor_gain0.9600

AlphaMissense

3245 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:152412189:G:CF15L0.995
1:152412189:G:TF15L0.995
1:152412191:A:GF15L0.995
1:152410869:G:CF71L0.994
1:152410869:G:TF71L0.994
1:152410871:A:GF71L0.994
1:152410860:G:CF74L0.991
1:152410860:G:TF74L0.991
1:152410862:A:GF74L0.991
1:152410870:A:GF71S0.990
1:152412136:A:GL33P0.989
1:152410861:A:GF74S0.988
1:152412112:A:GF41S0.987
1:152412127:A:GL36P0.986
1:152410832:C:GA84P0.982
1:152412124:A:GL37S0.981
1:152412151:A:TL28H0.981
1:152410837:G:TA82D0.979
1:152412190:A:GF15S0.979
1:152410838:C:GA82P0.978
1:152410870:A:CF71C0.978
1:152410861:A:CF74C0.976
1:152410845:A:CF79L0.974
1:152410845:A:TF79L0.974
1:152410847:A:GF79L0.974
1:152412132:T:AK34N0.971
1:152412132:T:GK34N0.971
1:152412223:A:GL4S0.971
1:152410852:A:GL77S0.968
1:152412100:A:TI45N0.968

dbSNP variants (sampled 300 via entrez): RS1001841905 (1:152412519 C>T), RS1002460077 (1:152413733 T>C), RS1002839986 (1:152414194 T>A), RS1002894393 (1:152414663 G>A,T), RS1002898178 (1:152414219 G>A), RS1003124119 (1:152411067 A>C), RS1003489060 (1:152412669 T>C), RS1003564747 (1:152411366 C>A,T), RS1004227898 (1:152408975 G>A,C), RS1004736408 (1:152415059 C>T), RS1005590598 (1:152412764 C>T), RS1005644332 (1:152410281 C>T), RS1005918438 (1:152414285 C>A,T), RS1006239297 (1:152411656 T>C), RS1006600955 (1:152411385 G>A)

Disease associations

OMIM: gene MIM:611312 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

9 associations (top):

StudyTraitp-value
GCST001960_3Eating disorders2.000000e-06
GCST003180_3Atopic march9.000000e-11
GCST007563_33Allergic disease (asthma, hay fever or eczema)3.000000e-11
GCST007564_24Asthma or allergic disease (pleiotropy)5.000000e-12
GCST008916_75Asthma2.000000e-08
GCST008916_82Asthma5.000000e-27
GCST008916_88Asthma1.000000e-25
GCST009798_76Asthma1.000000e-22
GCST012462_1Asthma and eczema2.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0007755atopic march

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

ChemicalActions (top 5)PubMed papers
Tobacco Smoke Pollutiondecreases expression, increases expression2
bisphenol Aaffects cotreatment, increases methylation1
sodium arsenatedecreases expression, increases abundance1
sodium arseniteaffects expression1
CGP 52608increases reaction, affects binding1
Resveratrolaffects cotreatment, decreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Acetaminophendecreases expression1
Aerosolsdecreases expression1
Arsenicdecreases expression, increases abundance1
Benzo(a)pyreneincreases methylation1
Methotrexateincreases expression1
Plant Extractsaffects cotreatment, decreases expression1
Ribonucleotidesaffects binding1
Sodium Dodecyl Sulfateincreases expression1
Tretinoinincreases expression1
Valproic Aciddecreases methylation1
Asbestos, Crocidoliteincreases expression1
Cadmium Chlorideincreases expression1

Clinical trials (associated diseases)

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