EPYC

gene
On this page

Also known as Pg-LbSLRR3B

Summary

EPYC (epiphycan, HGNC:3053) is a protein-coding gene on chromosome 12q21.33, encoding Epiphycan (Q99645). May have a role in bone formation and also in establishing the ordered structure of cartilage through matrix organization.

Dermatan sulfate proteoglycan 3 is a member of the small leucine-rich repeat proteoglycan family. This gene is composed of seven exons. It regulates fibrillogenesis by interacting with collagen fibrils and other extracellular matrix proteins.

Source: NCBI Gene 1833 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): schizophrenia (No Known Disease Relationship, GenCC)
  • Clinical variants (ClinVar): 67 total
  • MANE Select transcript: NM_004950

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:3053
Approved symbolEPYC
Nameepiphycan
Location12q21.33
Locus typegene with protein product
StatusApproved
AliasesPg-Lb, SLRR3B
Ensembl geneENSG00000083782
Ensembl biotypeprotein_coding
OMIM601657
Entrez1833

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 retained_intron

ENST00000261172, ENST00000550203, ENST00000551767

RefSeq mRNA: 1 — MANE Select: NM_004950 NM_004950

CCDS: CCDS31870

Canonical transcript exons

ENST00000261172 — 7 exons

ExonStartEnd
ENSE000007529869097004490970139
ENSE000007529879097282290972980
ENSE000010986889096368290964326
ENSE000010986919100240191002578
ENSE000036534349097808890978262
ENSE000037890399097180090972002
ENSE000038447389100494791004972

Expression profiles

Bgee: expression breadth broad, 61 present calls, max score 96.40.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 5.2844 / max 507.4572, expressed in 114 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
1325314.7416110
1325320.447874
1325300.095048

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cartilage tissueUBERON:000241896.40gold quality
tibiaUBERON:000097995.27gold quality
deciduaUBERON:000245094.89gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047382.99gold quality
stromal cell of endometriumCL:000225565.74gold quality
placentaUBERON:000198761.53gold quality
pancreatic ductal cellCL:000207960.82silver quality
hair follicleUBERON:000207352.43gold quality
mucosa of stomachUBERON:000119951.73gold quality
gall bladderUBERON:000211051.71gold quality
epithelial cell of pancreasCL:000008351.34gold quality
frontal poleUBERON:000279550.41gold quality
middle frontal gyrusUBERON:000270250.30gold quality
paraflocculusUBERON:000535150.18gold quality
Brodmann (1909) area 10UBERON:001354150.18gold quality
quadriceps femorisUBERON:000137750.01gold quality
metanephric glomerulusUBERON:000473649.61gold quality
ileal mucosaUBERON:000033149.45silver quality
vastus lateralisUBERON:000137949.45gold quality
layer of synovial tissueUBERON:000761649.45silver quality
Brodmann (1909) area 46UBERON:000648349.30gold quality
thymusUBERON:000237049.28gold quality
cerebellar vermisUBERON:000472049.25gold quality
cervix squamous epitheliumUBERON:000692249.20gold quality
olfactory bulbUBERON:000226448.92gold quality
myocardiumUBERON:000234948.87gold quality
type B pancreatic cellCL:000016948.83gold quality
cardiac muscle of right atriumUBERON:000337948.55gold quality
CA1 field of hippocampusUBERON:000388148.50gold quality
left ventricle myocardiumUBERON:000656648.24gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-CURD-112yes2218.10
E-ANND-3yes3.26

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): SOX9

miRNA regulators (miRDB)

34 targeting EPYC, 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-607799.9968.042299
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-477599.9875.006394
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-60799.9773.625593
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-590-3P99.9674.346478
HSA-MIR-335-3P99.9373.364958
HSA-MIR-367199.9073.043897
HSA-MIR-153-5P99.8973.866317
HSA-MIR-797899.8666.90856
HSA-MIR-5582-3P99.8672.484221
HSA-MIR-579-3P99.8671.663628
HSA-MIR-664B-3P99.8471.653590
HSA-MIR-1212999.7267.451311
HSA-MIR-425599.7267.701541
HSA-MIR-561-3P99.6470.903647
HSA-MIR-203A-3P99.4970.562806
HSA-MIR-372-5P99.4169.112299
HSA-MIR-3606-5P99.3169.671168
HSA-MIR-397399.2069.191990
HSA-MIR-452899.1869.771936
HSA-MIR-807799.1766.67862
HSA-MIR-371A-5P99.0866.511914
HSA-MIR-299-5P98.5671.141140
HSA-MIR-7852-3P98.3767.98823
HSA-MIR-124-5P98.1167.651095
HSA-MIR-6783-5P97.6767.211528
HSA-MIR-6818-5P97.5067.101167

Literature-anchored findings (GeneRIF, showing 5)

  • In addition, no pathogenic sequence variations were found in DCN, DSPG3, LUM, PITX2 and FOXC1, which have also been implicated in corneal and anterior segment dysgenesis. (PMID:17558846)
  • OPTC and EPYC are unlikely to play a major role in high myopia. (PMID:19844586)
  • Linkage and haplotype analyses identified 12q21.33 as a locus for posterior amorphous corneal dystrophy. However, no mutations were identified in the candidate genes (KERA, LUM, DCN, EPYC) within this region. (PMID:20357198)
  • KLF9 and EPYC acting as feature genes for osteoarthritis and their association with immune infiltration. (PMID:35902862)
  • EPYC functions as a novel prognostic biomarker for pancreatic cancer. (PMID:38184732)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioepycENSDARG00000056950
mus_musculusEpycENSMUSG00000019936
rattus_norvegicusEpycENSRNOG00000004717

Paralogs (10): OGN (ENSG00000106809), ECM2 (ENSG00000106823), FMOD (ENSG00000122176), OMG (ENSG00000126861), OMD (ENSG00000127083), LUM (ENSG00000139329), KERA (ENSG00000139330), PRELP (ENSG00000188783), LINGO4 (ENSG00000213171), LINGO3 (ENSG00000220008)

Protein

Protein identifiers

EpiphycanQ99645 (reviewed: Q99645)

Alternative names: Dermatan sulfate proteoglycan 3, Proteoglycan-Lb, Small chondroitin/dermatan sulfate proteoglycan

All UniProt accessions (2): Q99645, F8VSI4

UniProt curated annotations — full annotation on UniProt →

Function. May have a role in bone formation and also in establishing the ordered structure of cartilage through matrix organization.

Subcellular location. Secreted. Extracellular space. Extracellular matrix.

Tissue specificity. Cartilage, ligament, and placenta.

Post-translational modifications. The O-linked polysaccharides on Thr-60 and Ser-96 are probably the mucin type linked to GalNAc. There is one glycosaminoglycan chain, known to be dermatan sulfate, and it is probably the O-glycosylation at Ser-64.

Similarity. Belongs to the small leucine-rich proteoglycan (SLRP) family. SLRP class III subfamily.

RefSeq proteins (1): NP_004941* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000372LRRNTDomain
IPR001611Leu-rich_rptRepeat
IPR003591Leu-rich_rpt_typical-subtypRepeat
IPR032675LRR_dom_sfHomologous_superfamily
IPR043547Mimecan/Epiphycan/OpticinFamily

Pfam: PF00560, PF01462, PF13855

UniProt features (23 total): repeat 6, glycosylation site 5, sequence conflict 5, disulfide bond 2, signal peptide 1, chain 1, sequence variant 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q99645-F176.830.62

Functional residue map

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

Disulfide bonds (2): 118–130, 279–312

Glycosylation sites (5): 60, 64, 96, 283, 302

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 77 (showing top): GOBP_CARTILAGE_DEVELOPMENT, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_SENSORY_PERCEPTION_OF_MECHANICAL_STIMULUS, GOBP_BONE_DEVELOPMENT, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM5, chr12q21, GOBP_MULTI_MULTICELLULAR_ORGANISM_PROCESS, GOMF_GLYCOSAMINOGLYCAN_BINDING, AFP1_Q6, AACTTT_UNKNOWN, GOBP_SENSORY_PERCEPTION, GOBP_CONNECTIVE_TISSUE_DEVELOPMENT, FREAC7_01, TGGAAA_NFAT_Q4_01, GSE13762_CTRL_VS_125_VITAMIND_DAY12_DC_DN

GO Biological Process (4): female pregnancy (GO:0007565), sensory perception of sound (GO:0007605), bone development (GO:0060348), articular cartilage development (GO:0061975)

GO Molecular Function (2): glycosaminoglycan binding (GO:0005539), protein binding (GO:0005515)

GO Cellular Component (2): extracellular matrix (GO:0031012), extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
multi-organism reproductive process1
multi-multicellular organism process1
sensory perception of mechanical stimulus1
skeletal system development1
animal organ development1
cartilage development1
carbohydrate derivative binding1
binding1
external encapsulating structure1
cellular anatomical structure1

Protein interactions and networks

STRING

1098 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
EPYCBGNP13247622
EPYCLUMP51884602
EPYCLNPEPQ9UIQ6582
EPYCMATN4O95460560
EPYCHSPG2P98160557
EPYCFMODQ06828556
EPYCSTT3BQ8TCJ2507
EPYCNYXQ9GZU5490
EPYCACANP16112483
EPYCFN1P02751480
EPYCASPNQ9BXN1480
EPYCSTT3AP46977477
EPYCTGFBIQ15582471
EPYCECM2O94769465
EPYCTHBS4P35443465

IntAct

7 interactions, top by confidence:

ABTypeScore
CRKEPYCpsi-mi:“MI:0915”(physical association)0.490
EPYCPLCG2psi-mi:“MI:0915”(physical association)0.490
psi-mi:“MI:0914”(association)0.350

BioGRID (3): EPYC (Two-hybrid), EPYC (Two-hybrid), EPYC (Synthetic Lethality)

ESM2 similar proteins: A0N0X6, B1H134, B1H234, D3ZAL8, D3ZTV3, F1NUK7, O43155, O94769, O94991, P28653, P58874, P70186, P79119, Q32Q07, Q3MHH9, Q3SXY7, Q504C1, Q5FW85, Q5R482, Q5R6T0, Q5R7M3, Q5RAC4, Q61809, Q6RKD8, Q6UXK5, Q70AK3, Q7TNJ4, Q80ZD9, Q810B7, Q810B8, Q810C0, Q810C1, Q86SJ2, Q86VH5, Q8BGT1, Q8BLU0, Q8BZ81, Q8C110, Q8CBC6, Q8IW52

Diamond homologs: A3KNN3, A6H789, A6H793, A6NJW4, A8WHP9, E7FE13, F1MLX5, G5EFX6, O02678, O02833, O35367, O46378, O46379, O46542, O60938, O62702, O75093, O75094, O88279, O88280, O94813, P07359, P07585, P21793, P24014, P28654, P28675, P35858, P35859, P51884, P51885, P51886, P51888, P51890, P58874, P59034, P59035, P70186, P70389, P83286

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance55
Likely benign3
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

859 predictions. Top by Δscore:

VariantEffectΔscore
12:90964325:TT:Tacceptor_gain1.0000
12:90964327:C:CCacceptor_gain1.0000
12:90969700:C:CAdonor_gain1.0000
12:90971796:TTA:Tdonor_loss1.0000
12:90971797:TA:Tdonor_loss1.0000
12:90971798:A:ACdonor_gain1.0000
12:90971799:C:Adonor_loss1.0000
12:90971799:C:CAdonor_gain1.0000
12:90971799:CT:Cdonor_gain1.0000
12:90971799:CTT:Cdonor_gain1.0000
12:90971799:CTTT:Cdonor_gain1.0000
12:90971799:CTTTA:Cdonor_gain1.0000
12:90971998:ATCAC:Aacceptor_gain1.0000
12:90971999:TCAC:Tacceptor_gain1.0000
12:90972000:CAC:Cacceptor_gain1.0000
12:90972000:CACC:Cacceptor_gain1.0000
12:90972001:AC:Aacceptor_gain1.0000
12:90972002:CC:Cacceptor_gain1.0000
12:90972003:C:CCacceptor_gain1.0000
12:90972007:C:CTacceptor_gain1.0000
12:90972008:A:Tacceptor_gain1.0000
12:90972820:A:ACdonor_gain1.0000
12:90972821:C:CCdonor_gain1.0000
12:90972824:A:ACdonor_gain1.0000
12:90972824:AGG:Adonor_gain1.0000
12:90972825:G:Cdonor_gain1.0000
12:91002397:TTAC:Tdonor_loss1.0000
12:91002398:TA:Tdonor_loss1.0000
12:91002405:A:Cdonor_gain1.0000
12:91002574:CTTTC:Cacceptor_gain1.0000

AlphaMissense

2127 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:90964241:C:GR295P1.000
12:90970048:A:GL265P1.000
12:90964190:C:GC312S0.999
12:90964191:A:GC312R0.999
12:90964191:A:TC312S0.999
12:90964228:G:CN299K0.999
12:90964228:G:TN299K0.999
12:90964289:C:GC279S0.999
12:90964289:C:TC279Y0.999
12:90964290:A:GC279R0.999
12:90964290:A:TC279S0.999
12:90964292:A:CF278C0.999
12:90964321:G:CN268K0.999
12:90964321:G:TN268K0.999
12:90970048:A:TL265H0.999
12:90970054:A:GL263P0.999
12:90970101:G:CN247K0.999
12:90970101:G:TN247K0.999
12:90970117:A:GL242P0.999
12:90971839:A:CN221K0.999
12:90971839:A:TN221K0.999
12:90971909:A:GL198P0.999
12:90971915:A:GL196P0.999
12:90971981:A:GL174P0.999
12:90972932:C:GC130S0.999
12:90972932:C:TC130Y0.999
12:90972933:A:TC130S0.999
12:90964170:C:AG319W0.998
12:90964175:G:TP317H0.998
12:90964187:A:GL313P0.998

dbSNP variants (sampled 300 via entrez): RS1000016109 (12:91005926 G>A), RS1000018505 (12:90985058 G>T), RS1000049067 (12:90997238 T>C), RS1000093996 (12:91003020 G>A), RS1000149450 (12:91003327 A>C), RS1000176213 (12:90970495 C>G), RS1000219848 (12:90966928 C>T), RS1000252360 (12:90967194 A>C,G), RS1000275608 (12:90966968 C>A), RS1000399016 (12:90997021 T>C), RS1000452671 (12:90974113 T>C), RS1000585060 (12:90965856 C>A), RS1000826335 (12:90973830 G>A), RS1000899414 (12:90979050 C>G,T), RS1000929486 (12:90978965 G>A,T)

Disease associations

OMIM: gene MIM:601657 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
schizophreniaNo Known Disease RelationshipUnknown

Mondo (1): schizophrenia (MONDO:0005090)

Orphanet (0):

HPO phenotypes

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

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

15 total (human), top 15 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression1
cadmium sulfatedecreases expression1
CGP 52608affects binding, increases reaction1
entinostatincreases expression1
incobotulinumtoxinAincreases expression1
Arsenic Trioxidedecreases expression1
Atrazineincreases expression1
Benzo(a)pyrenedecreases expression1
Cycloheximidedecreases expression, decreases reaction1
Doxorubicinaffects expression1
Fluorouracilaffects expression1
T-2 Toxindecreases expression1
Tetrachlorodibenzodioxindecreases expression, decreases reaction1
Aflatoxin B1decreases methylation1
Okadaic Aciddecreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00000374PHASE4COMPLETEDTreatment for First-Episode Schizophrenia
NCT00001656PHASE4COMPLETEDComparison of Clozapine vs Olanzapine in Childhood-Onset Psychotic Disorders
NCT00007774PHASE4COMPLETEDTo Determine if Olanzapine is More Cost Effective Than Haloperidol for the Treatment of Schizophrenia
NCT00014001PHASE4COMPLETEDCATIE- Schizophrenia Trial
NCT00018668PHASE4COMPLETEDAntipsychotic Response in Schizophrenia
NCT00034801PHASE4COMPLETEDOlanzapine Versus Active Comparator in the Treatment of Depression in Patients With Schizophrenia
NCT00034905PHASE4COMPLETEDA Comparison of Seroquel vs. Risperidone in Schizophrenia
NCT00036088PHASE4COMPLETEDOlanzapine Versus An Active Comparator in the Treatment of Schizophrenia
NCT00044187PHASE4COMPLETEDThe Assessment of a Weight-Gain Agent for the Treatment of Olanzapine-Associated Anti-Obesity Agent in Patients With Schizophrenia, Schizophreniform Disorder, Schizoaffective Disorder, and Bipolar I Disorder
NCT00044655PHASE4COMPLETEDSwitching Medication to Treat Schizophrenia
NCT00048828PHASE4COMPLETEDTreating Drug-Resistant Childhood Schizophrenia
NCT00053703PHASE4COMPLETEDTreatment of Early Onset Schizophrenia Spectrum Disorders (TEOSS)
NCT00056498PHASE4COMPLETEDRisperidone Treatment in Schizophrenia Patients Who Are Currently Taking Clozapine
NCT00061802PHASE4COMPLETEDEfficacy and Safety of Two Atypical Antipsychotics vs. Placebo in Patients With an Acute Exacerbation of Either Schizophrenia or Schizoaffective Disorder
NCT00080327PHASE4COMPLETEDStudy of Three Doses of Aripiprazole in Patients With Acute Schizophrenia
NCT00088049PHASE4COMPLETEDStudy of Olanzapine vs. Aripiprazole in the Treatment of Schizophrenia
NCT00090012PHASE4COMPLETEDComparison of Continuing Olanzapine to Switching to Quetiapine in Overweight or Obese Patients With Schizophrenia and Schizoaffective Disorder
NCT00100776PHASE4COMPLETEDEfficacy of High Dose Olanzapine for the Treatment of Schizophrenia and Schizoaffective Disorder
NCT00103571PHASE4COMPLETEDOlanzapine Versus Aripiprazole in the Treatment of Acutely Ill Patients With Schizophrenia
NCT00108368PHASE4COMPLETEDThe Effects of Risperidone and Olanzapine on Thinking
NCT00114595PHASE4COMPLETEDEthyl-Eicosapentaenoic Acid and Tardive Dyskinesia
NCT00130923PHASE4COMPLETEDRisperidone Long-acting Versus Oral Risperidone in Patients With Schizophrenia and Alcohol Use Disorder
NCT00137020PHASE4COMPLETEDClinical Effect Of Cross Titration Of Antipsychotics With Ziprasidone In Schizophrenia Or Schizoaffective Disorder
NCT00140166PHASE4COMPLETEDTreatment of Acute Schizophrenia With Vitamin Therapy
NCT00145847PHASE4COMPLETEDNaltrexone Treatment of Alcohol Abuse in Schizophrenia
NCT00148564PHASE4COMPLETEDEnergy Homeostasis Under Treatment With Atypical Antipsychotics
NCT00156715PHASE4COMPLETEDEfficacy of Quetiapine in the Treatment of Patients With Schizophrenia and a Comorbid Substance Use Disorder
NCT00158223PHASE4COMPLETEDEffectiveness of Pimozide in Augmenting the Effects of Clozapine in the Treatment of Schizophrenia
NCT00159081PHASE4COMPLETEDOne Year Drug Treatment in First-Episode Schizophrenia
NCT00159120PHASE4COMPLETEDMaintenance Treatment vs. Stepwise Drug Discontinuation in First-Episode Schizophrenia
NCT00159133PHASE4COMPLETEDProdrome-Based Early Intervention With Antipsychotics vs. Benzodiazepines in First-Episode Schizophrenia
NCT00159757PHASE4TERMINATED12 Week Open, Non-Comparative Switch Study Of Oral Ziprazidone In Previously Treated Schizophrenic Patients
NCT00167817PHASE4COMPLETEDEffect of Switch to Aripiprazole on Health and Smoking Parameters in Patients With Schizophrenia: A Pilot Study
NCT00169026PHASE4TERMINATEDAlcoholism and Schizophrenia: Effects of Clozapine
NCT00169039PHASE4TERMINATEDClozapine Versus Chlorpromazine for Treatment-Unresponsive Schizophrenia
NCT00169065PHASE4COMPLETEDEffectiveness of Clozapine Versus Olanzapine for Treatment-resistant Schizophrenia
NCT00169091PHASE4TERMINATEDClozapine Versus Haloperidol for Treating the First Episode of Schizophrenia
NCT00176423PHASE4COMPLETEDEfficacy Study of Galantamine for Cognitive Impairments in Schizophrenia
NCT00176436PHASE4COMPLETEDAtomoxetine for Treatment of Weight Gain in Olanzapine or Clozapine Patients
NCT00177008PHASE4COMPLETEDAripiprazole for the Treatment of Schizophrenia With Co-Morbid Social Anxiety