Benign prostatic hyperplasia

disease
On this page

Also known as benign hyperplasia of prostatebenign hyperplasia of the prostatebenign prostate hyperplasiabenign prostatic hyperplasia (disease)benign prostatic hyperplasia - BPHbenign prostatic HypertrophyBPHprostate hypertrophyprostatic hyperplasia, benignprostatic hypertrophy

Summary

Benign prostatic hyperplasia (MONDO:0010811) is a disease with 32 cohort genes (149 GWAS associations across 37 studies) and 549 clinical trials. Top therapeutic interventions include tamsulosin, alfuzosin, and solifenacin.

At a glance

  • Cohort genes: 32
  • GWAS associations: 149
  • Clinical trials: 549

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical namebenign prostatic hyperplasia
Mondo IDMONDO:0010811
EFOEFO:0000284
MeSHD011470
OMIM600082
DOIDDOID:11132
ICD-10-CMN40
NCITC2897
SNOMED CT266569009
UMLSC1704272
MedGen312369
Anatomy (UBERON)UBERON:0002367
Is cancer (heuristic)no

Also known as: benign hyperplasia of prostate · benign hyperplasia of the prostate · benign prostate hyperplasia · benign prostatic hyperplasia · benign prostatic hyperplasia (disease) · benign prostatic hyperplasia - BPH · benign prostatic Hypertrophy · benign prostatic hypertrophy · BPH · prostate hypertrophy · prostatic hyperplasia, benign · prostatic hypertrophy

Data availability: 149 GWAS associations (37 studies) · 1 HPO phenotype · 11 cell lines.

Disease family

Classification path: disease › human disease › disease by body system or component › reproductive system disordermale reproductive system disorderprostate disorderbenign prostatic hyperplasia

Related subtypes (4): prostatic cyst, prostate calculus, prostatitis, prostate neoplasm

Genetics & variants

GWAS landscape

149 GWAS associations across 37 studies. Top hits map to 9 distinct genes (as reported by GWAS).

Top associations by p-value

rsIDp-valueGeneRisk alleleOdds ratio
chr10:1230476916e-49T0.08
chr5:13444581e-47G0.07
chr10:1230448312e-44T0.1
rs108869021e-43LINC01153 - RN7SKP167T0.09
rs24478535e-42CLPTM1LA0.06
rs108868948e-39LINC01153 - RN7SKP167T0.1
chr5:13220872e-38C0.08
rs110845964e-38LINC03103 - RNA5SP471T0.07
rs4149651e-32CLPTM1LG0.08
rs25563781e-28BCL11AT0.07
rs3819492e-28CLPTM1LG1.14
rs9715633e-28BCL11AT0.1
rs25563762e-26BCL11AC0.09
rs71246151e-24BET1LT0.13
rs4927153e-24SIRT3G0.11
rs1486788041e-22DNAJC1 - ADIPOR1P1A1.34
rs28536772e-22TERTG1.12
rs4654984e-22CLPTM1LA0.08
rs111998794e-20LINC01153 - RN7SKP167C1.13
chr10:1230452128e-20T0.09
chr10:223120495e-19G0.07
chr5:1346042152e-18A0.08
rs99586563e-18GATA6 - CTAGE1T1.11
chr8:234601233e-18A0.06
rs2004764e-17RSL24D1P1 - H4C10PA1.14
rs78989149e-17DNAJC1 - ADIPOR1P1A0.07
rs45485462e-16WDR11T1.11
chr6:1352887162e-16C0.05
chr18:199116903e-16G0.04
chr13:514923748e-16C0.07

Top studies (by case count)

StudyLead authorYearCasesControlsTitle
GCST90476153Verma A2024138,928243,435Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90475261Verma A202463,608229,593Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90475262Verma A202434,268258,933Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90478611Verma A202430,81364,576Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90480406Verma A202430,81364,576Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST007507Gudmundsson J201820,621280,541Genome-wide associations for benign prostatic hyperplasia reveal a genetic correlation with serum levels of PSA.
GCST007512Gudmundsson J201818,138277,213Genome-wide associations for benign prostatic hyperplasia reveal a genetic correlation with serum levels of PSA.
GCST90080617Backman JD202115,936156,384Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90084603Backman JD202115,936156,384Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90652192Liu TY202515,87884,916Diversity and longitudinal records: Genetic architecture of disease associations and polygenic risk in the Taiwanese Han population.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

TierVariants
Tier 1: coding0
Tier 2: splice/UTR0
Tier 3: regulatory0
Tier 4: intronic/intergenic50

MAF distribution

BucketVariants
common (>=0.05)48
low_freq (0.01-0.05)2
rare (<0.01)0
unknown0

Functional consequences

ConsequenceCount
unknown20
intergenic_variant15
intron_variant15

Top variants

rsIDChrPosAllelesMAFConsequenceGenep-valueTier
chr10:1230476910.2286e-49Tier 4: intronic/intergenic
chr5:13444580.4281e-47Tier 4: intronic/intergenic
chr10:1230448310.2292e-44Tier 4: intronic/intergenic
rs1088690210121289750T>A,C,G0.198intergenic_variantLINC01153 - RN7SKP1671e-43Tier 4: intronic/intergenic
rs244785351332962A>C,G,T0.443intron_variantCLPTM1L5e-42Tier 4: intronic/intergenic
rs1088689410121287359T>C0.207intergenic_variantLINC01153 - RN7SKP1678e-39Tier 4: intronic/intergenic
chr5:13220870.442e-38Tier 4: intronic/intergenic
rs110845961931614073T>C0.388intergenic_variantLINC03103 - RNA5SP4714e-38Tier 4: intronic/intergenic
rs41496551324006G>A0.407intron_variantCLPTM1L1e-32Tier 4: intronic/intergenic
rs2556378260535367T>A,C,G0.161intron_variantBCL11A1e-28Tier 4: intronic/intergenic
rs38194951322353G>A0.415intron_variantCLPTM1L2e-28Tier 4: intronic/intergenic
rs971563260547638T>A,C0.18intron_variantBCL11A3e-28Tier 4: intronic/intergenic
rs2556376260532897C>A,G,T0.193intron_variantBCL11A2e-26Tier 4: intronic/intergenic
rs712461511186604T>A,C0.16intergenic_variantBET1L1e-24Tier 4: intronic/intergenic
rs49271511232491G>T0.066intron_variantSIRT33e-24Tier 4: intronic/intergenic
rs1486788041022138360G>A,T0.035intergenic_variantDNAJC1 - ADIPOR1P11e-22Tier 4: intronic/intergenic
rs285367751287079G>A,C,T0.421intron_variantTERT2e-22Tier 4: intronic/intergenic
rs46549851325688A>C,G,T0.435intron_variantCLPTM1L4e-22Tier 4: intronic/intergenic
rs1119987910121285698T>A,C0.252intergenic_variantLINC01153 - RN7SKP1674e-20Tier 4: intronic/intergenic
chr10:1230452120.238e-20Tier 4: intronic/intergenic
chr10:223120490.2625e-19Tier 4: intronic/intergenic
chr5:1346042150.1232e-18Tier 4: intronic/intergenic
rs99586561822324181T>A,C0.43intron_variantGATA6 - CTAGE13e-18Tier 4: intronic/intergenic
chr8:234601230.4143e-18Tier 4: intronic/intergenic
rs200476627800570A>T0.162intergenic_variantRSL24D1P1 - H4C10P4e-17Tier 4: intronic/intergenic
rs78989141022038392A>G0.23intergenic_variantDNAJC1 - ADIPOR1P19e-17Tier 4: intronic/intergenic
rs454854610120870067C>G,T0.31intron_variantWDR112e-16Tier 4: intronic/intergenic
chr6:1352887160.3632e-16Tier 4: intronic/intergenic
chr18:199116900.4453e-16Tier 4: intronic/intergenic
chr13:514923740.0738e-16Tier 4: intronic/intergenic

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 58 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
TBX3Orphanet:3138Ulnar-mammary syndrome
TBX5Orphanet:101016Romano-Ward syndrome
TBX5Orphanet:392Holt-Oram syndrome
HNF1BOrphanet:1309Medullary sponge kidney
HNF1BOrphanet:1331Familial prostate cancer
HNF1BOrphanet:2578Mayer-Rokitansky-Küster-Hauser syndrome type 2
HNF1BOrphanet:26126517q12 microdeletion syndrome
HNF1BOrphanet:93111HNF1B-related autosomal dominant tubulointerstitial kidney disease
HNF1BOrphanet:93172Renal dysplasia, unilateral
HNF1BOrphanet:93173Renal dysplasia, bilateral
HNF1BOrphanet:97363Unilateral multicystic dysplastic kidney
HNF1BOrphanet:97364Bilateral multicystic dysplastic kidney
TERTOrphanet:146Differentiated thyroid carcinoma
TERTOrphanet:1501Adrenocortical carcinoma
TERTOrphanet:1775Dyskeratosis congenita
TERTOrphanet:2032Idiopathic pulmonary fibrosis
TERTOrphanet:2495Meningioma
TERTOrphanet:3322Hoyeraal-Hreidarsson syndrome
TERTOrphanet:457246Clear cell sarcoma of kidney
TERTOrphanet:618Familial melanoma
TERTOrphanet:88Idiopathic aplastic anemia
BCL11AOrphanet:251380Hereditary persistence of fetal hemoglobin-sickle cell disease syndrome
BCL11AOrphanet:619233Hereditary persistence of fetal hemoglobin-intellectual disability syndrome
PHIPOrphanet:589905PHIP-related behavioral problems-intellectual disability-obesity-dysmorphic features syndrome
GATA5Orphanet:3303Tetralogy of Fallot
GATA5Orphanet:334Hereditary atrial fibrillation
GATA5Orphanet:402075Familial bicuspid aortic valve
UNC13AOrphanet:803Amyotrophic lateral sclerosis
RNASEH2BOrphanet:51Aicardi-Goutières syndrome
RNASEH2BOrphanet:689234RNASEH2B-related hereditary spastic paraplegia
DCCOrphanet:238722Familial congenital mirror movements
DCCOrphanet:2744Horizontal gaze palsy with progressive scoliosis
DCCOrphanet:478Kallmann syndrome
FGFR2Orphanet:1540Jackson-Weiss syndrome
FGFR2Orphanet:1555Cutis gyrata-acanthosis nigricans-craniosynostosis syndrome
FGFR2Orphanet:168624Familial scaphocephaly syndrome, McGillivray type
FGFR2Orphanet:207Crouzon syndrome
FGFR2Orphanet:2363Lacrimoauriculodentodigital syndrome
FGFR2Orphanet:313855FGFR2-related bent bone dysplasia
FGFR2Orphanet:596008Antley-Bixler syndrome without genital anomaly or disorder of steroidogenesis
FGFR2Orphanet:794Saethre-Chotzen syndrome
FGFR2Orphanet:87Apert syndrome
FGFR2Orphanet:93258Pfeiffer syndrome type 1
FGFR2Orphanet:93259Pfeiffer syndrome type 2
FGFR2Orphanet:93260Pfeiffer syndrome type 3
GATA3Orphanet:2237Hypoparathyroidism-sensorineural deafness-renal disease syndrome
GATA3Orphanet:585936B-lymphoblastic leukemia/lymphoma with hyperdiploidy
GATA6Orphanet:2140Congenital diaphragmatic hernia
GATA6Orphanet:2255Pancreatic hypoplasia-diabetes-congenital heart disease syndrome
GATA6Orphanet:3303Tetralogy of Fallot

Cohort genes → proteins

32 cohort genes, 29 distinct canonical proteins.

Evidence partition

SubsetGenes
gwas_only32

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
SYN3HGNC:11496ENSG00000185666O14994Synapsin-3gwas
TBX3HGNC:11602ENSG00000135111O15119T-box transcription factor TBX3gwas
TBX5HGNC:11604ENSG00000089225Q99593T-box transcription factor TBX5gwas
HNF1BHGNC:11630ENSG00000275410P35680Hepatocyte nuclear factor 1-betagwas
TERTHGNC:11730ENSG00000164362O14746Telomerase reverse transcriptasegwas
UGCGHGNC:12524ENSG00000148154Q16739Ceramide glucosyltransferasegwas
BCL11AHGNC:13221ENSG00000119866Q9H165BCL11 transcription factor Agwas
DLEU1HGNC:13747ENSG00000176124O43261Leukemia-associated protein 1gwas
PHIPHGNC:15673ENSG00000146247Q8WWQ0PH-interacting proteingwas
GATA5HGNC:15802ENSG00000130700Q9BWX5Transcription factor GATA-5gwas
ELOVL6HGNC:15829ENSG00000170522Q9H5J4Very long chain fatty acid elongase 6gwas
BTBD3HGNC:15854ENSG00000132640Q9Y2F9BTB/POZ domain-containing protein 3gwas
SPTLC3HGNC:16253ENSG00000172296Q9NUV7Serine palmitoyltransferase 3gwas
SORCS1HGNC:16697ENSG00000108018Q8WY21VPS10 domain-containing receptor SorCS1gwas
STARD4HGNC:18058ENSG00000164211Q96DR4StAR-related lipid transfer protein 4gwas
CIMAP1AHGNC:19905ENSG00000177947Q96PU9Ciliary microtubule associated protein 1Agwas
DNAJC1HGNC:20090ENSG00000136770Q96KC8DnaJ homolog subfamily C member 1gwas
UNC13AHGNC:23150ENSG00000130477Q9UPW8Protein unc-13 homolog Agwas
CLPTM1LHGNC:24308ENSG00000049656Q96KA5Lipid scramblase CLPTM1Lgwas
CTAGE1HGNC:24346ENSG00000212710Q96RT6cTAGE family member 2gwas
RNASEH2BHGNC:25671ENSG00000136104Q5TBB1Ribonuclease H2 subunit Bgwas
DCCHGNC:2701ENSG00000187323P43146Netrin receptor DCCgwas
FGFR2HGNC:3689ENSG00000066468P21802Fibroblast growth factor receptor 2gwas
MIR3134HGNC:38254ENSG00000264354microRNA 3134gwas
EBLN1HGNC:39430ENSG00000223601P0CF75Endogenous Bornavirus-like nucleoprotein 1gwas
GATA3HGNC:4172ENSG00000107485P23771Trans-acting T-cell-specific transcription factor GATA-3gwas
GATA6HGNC:4174ENSG00000141448Q92908Transcription factor GATA-6gwas
GCLCHGNC:4311ENSG00000001084P48506Glutamate–cysteine ligase catalytic subunitgwas
MACROH2A1HGNC:4740ENSG00000113648O75367Core histone macro-H2A.1gwas
H2BC13HGNC:4748ENSG00000185130Q99880Histone H2B type 1-Lgwas
LINC03103HGNC:48330ENSG00000267465long intergenic non-protein coding RNA 3103gwas
PITX1-AS1HGNC:48332ENSG00000224186PITX1 antisense RNA 1gwas

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
SYN3Synapsin-3May be involved in the regulation of neurotransmitter release and synaptogenesis.
TBX3T-box transcription factor TBX3Transcriptional repressor involved in developmental processes.
TBX5T-box transcription factor TBX5DNA-binding protein that regulates the transcription of several genes and is involved in heart development and limb pattern formation.
HNF1BHepatocyte nuclear factor 1-betaTranscription factor that binds to the inverted palindrome 5’-GTTAATNATTAAC-3'.
TERTTelomerase reverse transcriptaseTelomerase is a ribonucleoprotein enzyme essential for the replication of chromosome termini in most eukaryotes.
UGCGCeramide glucosyltransferaseParticipates in the initial step of the glucosylceramide-based glycosphingolipid/GSL synthetic pathway at the cytosolic surface of the Golgi.
BCL11ABCL11 transcription factor ATranscription factor.
DLEU1Leukemia-associated protein 1May act as a tumor suppressor.
PHIPPH-interacting proteinProbable regulator of the insulin and insulin-like growth factor signaling pathways.
GATA5Transcription factor GATA-5Transcription factor required during cardiovascular development.
ELOVL6Very long chain fatty acid elongase 6Catalyzes the first and rate-limiting reaction of the four reactions that constitute the long-chain fatty acids elongation cycle.
BTBD3BTB/POZ domain-containing protein 3Acts as a key regulator of dendritic field orientation during development of sensory cortex.
SPTLC3Serine palmitoyltransferase 3Component of the serine palmitoyltransferase multisubunit enzyme (SPT) that catalyzes the initial and rate-limiting step in sphingolipid biosynthesis by condensing L-serine and activated acyl-CoA (most commonly palmitoyl-CoA) to form long-…
STARD4StAR-related lipid transfer protein 4Involved in the intracellular transport of cholesterol.
CIMAP1ACiliary microtubule associated protein 1AOuter dense fibers are filamentous structures located on the outside of the axoneme in the midpiece and principal piece of the mammalian sperm tail.
DNAJC1DnaJ homolog subfamily C member 1May modulate protein synthesis.
UNC13AProtein unc-13 homolog APlays a role in vesicle maturation during exocytosis as a target of the diacylglycerol second messenger pathway.
CLPTM1LLipid scramblase CLPTM1LScramblase that mediates the translocation of glucosaminylphosphatidylinositol (alpha-D-GlcN-(1-6)-(1,2-diacyl-sn-glycero-3-phospho)-1D-myo-inositol, GlcN-PI) across the endoplasmic reticulum (ER) membrane, from the cytosolic leaflet to th…
RNASEH2BRibonuclease H2 subunit BNon catalytic subunit of RNase H2, an endonuclease that specifically degrades the RNA of RNA:DNA hybrids.
DCCNetrin receptor DCCReceptor for netrin required for axon guidance.
FGFR2Fibroblast growth factor receptor 2Tyrosine-protein kinase that acts as a cell-surface receptor for fibroblast growth factors and plays an essential role in the regulation of cell proliferation, differentiation, migration and apoptosis, and in the regulation of embryonic de…
EBLN1Endogenous Bornavirus-like nucleoprotein 1May act as an RNA-binding protein.
GATA3Trans-acting T-cell-specific transcription factor GATA-3Transcriptional activator which binds to the enhancer of the T-cell receptor alpha and delta genes.
GATA6Transcription factor GATA-6Transcriptional activator.
GCLCGlutamate–cysteine ligase catalytic subunitCatalyzes the ATP-dependent ligation of L-glutamate and L-cysteine and participates in the first and rate-limiting step in glutathione biosynthesis.
MACROH2A1Core histone macro-H2A.1Variant histone H2A which replaces conventional H2A in a subset of nucleosomes where it represses transcription.
H2BC13Histone H2B type 1-LCore component of nucleosome.

Protein-family classification

Druggable: 8 · Difficult: 9 · Unknown: 15 · Druggable fraction: 0.25

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

FamilyGenesFoldFDR
Transcription factor82.1×0.200
Enzyme (other)51.9×0.371
Antibody/Immunoglobulin21.8×0.600
Kinase10.9×0.884
Other/Unknown150.8×0.884
Scaffold/PPI10.5×0.884

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
SYN3Other/UnknownnoSynapsin, ATP_grasp_subdomain_1, PreATP-grasp_dom_sf
TBX3Transcription factornoTF_T-box, p53-like_TF_DNA-bd_sf, TF_T-box_CS
TBX5Transcription factornoTF_T-box, p53-like_TF_DNA-bd_sf, TF_T-box_CS
HNF1BTranscription factornoHD, HNF1b_C, HNF-1_N
TERTOther/UnknownnoRT_dom, Telomerase_RT, Telomerase_RBD
UGCGEnzyme (other)yes2.4.1.80Ceramide_glucosylTrfase, Nucleotide-diphossugar_trans
BCL11ATranscription factornoZnf_C2H2_type, Znf_C2H2_sf, Dev/Hematopoietic_TF
DLEU1Other/Unknownno
PHIPScaffold/PPInoBromodomain, WD40_rpt, WD40/YVTN_repeat-like_dom_sf
GATA5Transcription factornoZnf_GATA, GATA_N, Znf_NHR/GATA
ELOVL6Enzyme (other)yes2.3.1.16ELO_fam, ELO_CS, ELOVL6
BTBD3Other/UnknownnoBTB/POZ_dom, SKP1/BTB/POZ_sf, BACK
SPTLC3Enzyme (other)yes2.3.1.50Aminotrans_II_pyridoxalP_BS, Aminotransferase_I/II_large, PyrdxlP-dep_Trfase_major
SORCS1Antibody/ImmunoglobulinyesPKD_dom, VPS10, Ig-like_fold
STARD4Other/UnknownnoSTART_lipid-bd_dom, START-like_dom_sf, StarD4
CIMAP1AOther/UnknownnoSHIPPO-rpt, CIMAP
DNAJC1Transcription factornoSANT/Myb, DnaJ_domain, Homeodomain-like_sf
UNC13AOther/UnknownnoC2_dom, PKC_DAG/PE, MUN_dom
CLPTM1LOther/UnknownnoCLPTM1
CTAGE1Other/UnknownnocTAGE_MIA/OTOR
RNASEH2BEnzyme (other)yes3.1.26.4RNase_H2_suB_wHTH, RNase_H2_suB, Rnh202_N
DCCAntibody/ImmunoglobulinyesIg_sub2, Ig_sub, FN3_dom
FGFR2Kinaseyes2.7.10.1Prot_kinase_dom, Ser-Thr/Tyr_kinase_cat_dom, Ig_sub2
MIR3134Other/Unknownno
EBLN1Other/UnknownnoP40_nucleoprot_BD-vir, P40_nucleoprot_sub1_BD-vir, P40_nucleoprot_sub2_BD-vir
GATA3Transcription factornoZnf_GATA, Znf_NHR/GATA, TF_GATA-2/3
GATA6Transcription factornoZnf_GATA, GATA_N, Znf_NHR/GATA
GCLCEnzyme (other)yes6.3.2.2GCS, Gln_synth/guanido_kin_cat_dom
MACROH2A1Other/UnknownnoHistone_H2A, Macro_dom, H2A/H2B/H3
H2BC13Other/UnknownnoHistone_H2B, H2A/H2B/H3, Histone-fold
LINC03103Other/Unknownno
PITX1-AS1Other/Unknownno

Expression context

Cohort genes with no expression data: 0.

23 cohort genes are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

BucketGenes
narrow (1-5 tissues)0
moderate (6-20)2
broad (>20)30
unknown0

Top tissues across cohort

TissueCohort genes
adrenal tissue5
cortical plate4
right testis4
primordial germ cell in gonad3
buccal mucosa cell3
bronchial epithelial cell3
male germ line stem cell (sensu Vertebrata) in testis3
ileal mucosa3
jejunal mucosa3
left testis3
primary visual cortex2
upper leg skin2
ganglionic eminence2
ventricular zone2
kidney epithelium2
adrenal cortex1
right adrenal gland1
right adrenal gland cortex1
cardiac muscle of right atrium1
tendon of biceps brachii1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
SYN3176broadmarkerprimordial germ cell in gonad, cortical plate, primary visual cortex
TBX3243ubiquitousmarkerright adrenal gland cortex, right adrenal gland, adrenal cortex
TBX5129broadmarkertendon of biceps brachii, cardiac muscle of right atrium, buccal mucosa cell
HNF1B74broadmarkermetanephros cortex, adult mammalian kidney, kidney
TERT105broadyesstromal cell of endometrium, type B pancreatic cell, olfactory bulb
UGCG274ubiquitousmarkerupper leg skin, bronchial epithelial cell, adrenal tissue
BCL11A247ubiquitousmarkercortical plate, ganglionic eminence, primary visual cortex
DLEU1162ubiquitousmarkerprimordial germ cell in gonad, male germ line stem cell (sensu Vertebrata) in testis, islet of Langerhans
PHIP302ubiquitousmarkerbronchial epithelial cell, epithelium of bronchus, ventricular zone
GATA5106broadyesileal mucosa, left uterine tube, jejunal mucosa
ELOVL6255ubiquitousmarkerright lobe of liver, endothelial cell, esophagus squamous epithelium
BTBD3298ubiquitousmarkercerebellar vermis, adrenal tissue, paraflocculus
SPTLC3228ubiquitousmarkerbuccal mucosa cell, placenta, skin of abdomen
SORCS1188broadmarkercortical plate, sural nerve, trigeminal ganglion
STARD4221ubiquitousmarkeradrenal tissue, ileal mucosa, jejunal mucosa
CIMAP1A28yesleft ventricle myocardium, kidney epithelium, epithelial cell of pancreas
DNAJC1278ubiquitousmarkersecondary oocyte, pylorus, cardia of stomach
UNC13A193broadmarkerright hemisphere of cerebellum, cerebellar hemisphere, cerebellar cortex
CLPTM1L255ubiquitousmarkerileal mucosa, kidney epithelium, right lobe of thyroid gland
CTAGE113tissue_specificyesright testis, left testis, testis
RNASEH2B242ubiquitousmarkercalcaneal tendon, ganglionic eminence, ventricular zone
DCC154broadmarkercortical plate, right testis, left testis
FGFR2272broadmarkerC1 segment of cervical spinal cord, spinal cord, corpus callosum
MIR313466yesadrenal tissue, blood, putamen
EBLN17yesprimordial germ cell in gonad, male germ line stem cell (sensu Vertebrata) in testis, right testis
GATA3220broadmarkerupper leg skin, skin of hip, endometrium epithelium
GATA6204ubiquitousmarkergerminal epithelium of ovary, parietal pleura, jejunal mucosa
GCLC291ubiquitousmarkerbronchial epithelial cell, right uterine tube, olfactory segment of nasal mucosa
MACROH2A1302ubiquitousmarkerepithelium of nasopharynx, tongue squamous epithelium, monocyte
H2BC13130ubiquitousyesbone marrow cell, adrenal tissue, male germ line stem cell (sensu Vertebrata) in testis

Protein interactions among cohort

Intra-cohort edges: 5.

Hub genes (top 10 by interactor count)

SymbolInteractor count
GATA35,990
TERT5,717
PHIP3,057
MACROH2A13,047
H2BC132,784
GATA52,434
BCL11A2,389
TBX32,379
DNAJC12,375
TBX52,250

Intra-cohort edges

ABSources
BCL11AFGFR2intact
CLPTM1LTERTstring_interaction
GATA5TBX5string_interaction
SPTLC3UGCGstring_interaction
TBX3TBX5string_interaction

Structural data

PDB: 14 · AlphaFold-only: 15 · No structure: 3

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
PHIPQ8WWQ0146
FGFR2P2180263
TERTO1474623
BCL11AQ9H16517
MACROH2A1O7536713
DCCP431469
TBX5Q995934
RNASEH2BQ5TBB14
HNF1BP356803
GATA3P237713
STARD4Q96DR42
DNAJC1Q96KC82
SYN3O149941
TBX3O151191

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
GCLCP4850693.68
UGCGQ1673993.29
ELOVL6Q9H5J492.40
H2BC13Q9988087.45
SPTLC3Q9NUV787.25
EBLN1P0CF7584.45
BTBD3Q9Y2F983.60
CLPTM1LQ96KA578.54
SORCS1Q8WY2177.77
CIMAP1AQ96PU974.04
UNC13AQ9UPW873.58
CTAGE1Q96RT670.45
GATA5Q9BWX559.91
DLEU1O4326155.08
GATA6Q9290853.48

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 145. Enrichment computed across 32 evidence-associated genes (18 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 18 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Signaling by FGFR2 amplification mutants1634.4×0.057FGFR2
Signaling by FGFR2 fusions1634.4×0.057FGFR2
Developmental Lineage of Multipotent Pancreatic Progenitor Cells266.8×0.057HNF1B, GATA6
Cardiogenesis247.0×0.057TBX5, GATA6
Factors involved in megakaryocyte development and platelet production311.1×0.067GATA5, GATA3, GATA6
Defective GCLC causes HAGGSD1317.2×0.076GCLC
Sphingolipid metabolism218.7×0.104UGCG, SPTLC3
DSCAM interactions1126.9×0.107DCC
Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence190.6×0.107TERT
Regulation of gene expression in early pancreatic precursor cells179.3×0.107HNF1B
Netrin mediated repulsion signals170.5×0.107DCC
FGFR2b ligand binding and activation163.4×0.107FGFR2
POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation163.4×0.107GATA6
Caspase activation via Dependence Receptors in the absence of ligand163.4×0.107DCC
Role of second messengers in netrin-1 signaling157.7×0.107DCC
Glutathione synthesis and recycling152.9×0.107GCLC
Regulation of commissural axon pathfinding by SLIT and ROBO152.9×0.107DCC
ALK mutants bind TKIs152.9×0.107BCL11A
FGFR2c ligand binding and activation148.8×0.107FGFR2
Nephron development148.8×0.107HNF1B
Pregnenolone biosynthesis145.3×0.107STARD4
YAP1- and WWTR1 (TAZ)-stimulated gene expression142.3×0.107TBX5
Developmental Lineage of Mammary Stem Cells142.3×0.107GATA3
Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells139.6×0.107HNF1B
DCC mediated attractive signaling139.6×0.107DCC
Formation of definitive endoderm139.6×0.107GATA6
Activated point mutants of FGFR2137.3×0.107FGFR2
Physiological factors137.3×0.107TBX5
Serotonin Neurotransmitter Release Cycle135.2×0.107SYN3
Phospholipase C-mediated cascade; FGFR2135.2×0.107FGFR2

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 27 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
hepatoblast differentiation2624.1×6e-04TBX3, HNF1B
cell fate commitment443.8×6e-04GATA5, FGFR2, GATA3, GATA6
atrioventricular bundle cell differentiation2416.1×0.001TBX3, TBX5
positive regulation of cardiac muscle cell proliferation369.3×0.001TBX5, FGFR2, GATA6
cellular response to BMP stimulus362.4×0.001GATA5, GATA3, GATA6
in utero embryonic development513.3×0.003TBX3, RNASEH2B, FGFR2, GATA3, GATA6
sinoatrial node development2156.0×0.004TBX5, GATA6
forelimb morphogenesis2156.0×0.004TBX3, TBX5
negative regulation of dendrite development2156.0×0.004BCL11A, DCC
negative regulation of transcription by RNA polymerase II85.2×0.004TBX3, HNF1B, BCL11A, GATA5, FGFR2, GATA3, GATA6, MACROH2A1
atrioventricular canal development2113.5×0.005TBX3, GATA6
negative regulation of collateral sprouting2113.5×0.005BCL11A, DCC
intestinal epithelial cell differentiation2113.5×0.005GATA5, GATA6
positive regulation of transcription by RNA polymerase II84.4×0.010TBX3, TBX5, BCL11A, PHIP, GATA5, FGFR2, GATA3, GATA6
embryonic digestive tract morphogenesis269.3×0.012HNF1B, FGFR2
smooth muscle cell differentiation265.7×0.013TBX3, GATA6
RNA-templated transcription1624.1×0.013TERT
type IV hypersensitivity1624.1×0.013GATA3
ribonucleotide metabolic process1624.1×0.013RNASEH2B
cholesterol transport involved in cholesterol storage1624.1×0.013STARD4
DNA strand elongation1624.1×0.013TERT
negative regulation of transforming growth factor beta2 production1624.1×0.013GATA6
tube morphogenesis1624.1×0.013GATA6
regulation of pronephros size1624.1×0.013HNF1B
fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow cell1624.1×0.013FGFR2
fibroblast growth factor receptor signaling pathway involved in hemopoiesis1624.1×0.013FGFR2
fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow1624.1×0.013FGFR2
pronephric nephron tubule development1624.1×0.013HNF1B
sphingoid biosynthetic process1624.1×0.013SPTLC3
mesoderm morphogenesis1624.1×0.013TBX3

Therapeutics

Drugs indicated for this disease

7 approved, 7 in late-stage (phase 3) trials. Disease-direct ChEMBL indications, not inferred from the associated-gene cohort below.

DrugDevelopment status
AlfuzosinApproved (phase 4)
DutasterideApproved (phase 4)
FinasterideApproved (phase 4)
SilodosinApproved (phase 4)
TadalafilApproved (phase 4)
TamsulosinApproved (phase 4)
TerazosinApproved (phase 4)
CetrorelixPhase 3 (in late-stage trials)
DoxazosinPhase 3 (in late-stage trials)
FexapotidePhase 3 (in late-stage trials)
LonidaminePhase 3 (in late-stage trials)
Saw PalmettoPhase 3 (in late-stage trials)
SolifenacinPhase 3 (in late-stage trials)
TopsalysinPhase 3 (in late-stage trials)

Earlier-phase candidates (phase 2, investigational — efficacy not yet established): Adalimumab, Celecoxib, Degarelix, Epigalocatechin Gallate, Etonogestrel, Lycopene, Onabotulinumtoxina, Ozarelix, Paclitaxel, Sildenafil, Sodium Chloride, Tertomotide, Vardenafil.

Drug target analysis

Approved (phase 4): 3 · Phase ≥3: 3 · Phased (≥1): 4 · Undrugged: 28

Druggability breadth: 10 of 32 evidence-associated genes (31%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Genes with an approved drug

The molecule shown is one approved compound that hits the gene — not necessarily a drug of choice or one indicated for this disease.

SymbolExample approved molecule
TERTBERBERINE
UGCGMIGLUSTAT
FGFR2PONATINIB

Top cohort targets by molecule count

SymbolMoleculesMax phase
FGFR2594
TERT104
UGCG54
GCLC11
SYN300
TBX300
TBX500
HNF1B00
BCL11A00
DLEU100

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
BERBERINE4TERT
DOXORUBICIN4TERT
MIGLUSTAT4UGCG
ELIGLUSTAT4UGCG
PONATINIB4FGFR2
PEMIGATINIB4FGFR2
NINTEDANIB4FGFR2
FEDRATINIB4FGFR2
LENVATINIB4FGFR2
AXITINIB4FGFR2
SORAFENIB4FGFR2
INFIGRATINIB PHOSPHATE4FGFR2
INFIGRATINIB4FGFR2
IBRUTINIB4FGFR2
CERITINIB4FGFR2
VANDETANIB4FGFR2
NINTEDANIB ESYLATE4FGFR2
BRIGATINIB4FGFR2
ERDAFITINIB4FGFR2
FUTIBATINIB4FGFR2
PAZOPANIB4FGFR2
SUNITINIB4FGFR2
DASATINIB4FGFR2
ERLOTINIB4FGFR2
MIDOSTAURIN4FGFR2
RESVERATROL3TERT
EPIGALOCATECHIN GALLATE3TERT
PERIFOSINE3TERT
LUCERASTAT3UGCG
VENGLUSTAT3UGCG

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 6.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

SymbolAssaysType breakdown
FGFR2966Binding:940, Functional:22, ADMET:4
TERT391Binding:389, Functional:2
UGCG44Binding:41, Functional:3
PHIP17Binding:17
GCLC14Binding:14
ELOVL610Binding:10
TBX51Binding:1
SPTLC31Binding:1
CLPTM1L1Binding:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
UGCG2.4.1.80ceramide glucosyltransferase
ELOVL62.3.1.16, 2.3.1.199acetyl-CoA C-acyltransferase, very-long-chain 3-oxoacyl-CoA synthase
SPTLC32.3.1.50serine C-palmitoyltransferase
RNASEH2B3.1.26.4ribonuclease H
FGFR22.7.10.1receptor protein-tyrosine kinase
GCLC6.3.2.2glutamate-cysteine ligase

Cohort genes with high screening signal

≥100 ChEMBL assays — a studied-ness signal; see Therapeutics for approved-drug status.

SymbolChEMBL assays
TERT391
FGFR2966

Pharmacogenomics

Cohort genes with a PharmGKB record: 30; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

30 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

CompoundMax phaseCohort target (bioactivity)
BERBERINE4TERT
DOXORUBICIN4TERT
MIGLUSTAT4UGCG
ELIGLUSTAT4UGCG
PONATINIB4FGFR2
PEMIGATINIB4FGFR2
NINTEDANIB4FGFR2
FEDRATINIB4FGFR2
LENVATINIB4FGFR2
AXITINIB4FGFR2
SORAFENIB4FGFR2
INFIGRATINIB PHOSPHATE4FGFR2
INFIGRATINIB4FGFR2
IBRUTINIB4FGFR2
CERITINIB4FGFR2
VANDETANIB4FGFR2
NINTEDANIB ESYLATE4FGFR2
BRIGATINIB4FGFR2
ERDAFITINIB4FGFR2
FUTIBATINIB4FGFR2
PAZOPANIB4FGFR2
SUNITINIB4FGFR2
DASATINIB4FGFR2
ERLOTINIB4FGFR2
MIDOSTAURIN4FGFR2
RESVERATROL3TERT
EPIGALOCATECHIN GALLATE3TERT
PERIFOSINE3TERT
LUCERASTAT3UGCG
VENGLUSTAT3UGCG

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

TierDefinitionGenesSymbols
AApproved (phase 4 drug)3TERT, UGCG, FGFR2
BPhased (≥1) drug, not yet approved1GCLC
CDruggable family + PDB, no drug2RNASEH2B, DCC
DDruggable family + AlphaFold only, no drug3ELOVL6, SPTLC3, SORCS1
EDifficult family or no structure, no drug23SYN3, TBX3, TBX5, HNF1B, BCL11A, DLEU1, PHIP, GATA5, BTBD3, STARD4 (+13 more)

Undrugged target profiles

28 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

SymbolChEMBL assaysDrugged partners (top 3)
CLPTM1L1TERT
SYN30
TBX30
TBX51
HNF1B0
BCL11A0
DLEU10
PHIP17
GATA50
ELOVL610
BTBD30
SPTLC31
SORCS10
STARD40
CIMAP1A0
DNAJC10
UNC13A0
CTAGE10
RNASEH2B0
DCC0
MIR31340
EBLN10
GATA30
GATA60
MACROH2A10
H2BC130
LINC031030
PITX1-AS10

Clinical trials & evidence

Clinical trials

Clinical trials: 549.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified333
PHASE465
PHASE361
PHASE242
PHASE126
PHASE1/PHASE210
PHASE2/PHASE37
EARLY_PHASE15

Top trials by phase / activity

NCTPhaseStatusTitle
NCT06710327PHASE4NOT_YET_RECRUITINGEffect of Tranexamic Acid on Intraoperative Blood Loss in Patients Undergoing Aquablation
NCT07204002PHASE4NOT_YET_RECRUITINGComparison of Convective Water Vapor Ablation (Convective Water Vapor Energy, WAVE™) With the Rezum™ System Versus Holmium Laser Enucleation of the Prostate (HoLEP) Versus Bipolar Transurethral Resection of the Prostate (TUR-P) in Patients With Benign Prostatic Syndrome (BPS) - A Randomized Study
NCT07357324PHASE4RECRUITINGA Clinical Observation Study of a Chinese Patent Medicine Combined With Tamsulosin in Improving Sleep and Nocturia Symptoms After Enucleation of the Prostate
NCT07460518PHASE4NOT_YET_RECRUITINGTranexamic Acid for Bleeding Reduction During TURP Surgery
NCT07467343PHASE4NOT_YET_RECRUITINGSilodosin vs Tamsulosin for LUTS Due to BPH: A Randomized Crossover Trial
NCT00130767PHASE4UNKNOWNKinetics of the Finasteride Prostate Induced Apoptosis
NCT00194675PHASE4COMPLETEDTRADE-Testosterone Replacement and Dutasteride Effectiveness
NCT00199550PHASE4COMPLETEDBipolar vs Monopolar Transurethral Resection of the Prostate (TURP)
NCT00364585PHASE4COMPLETEDA Prospective Evaluation of the GreenLight Model 120 Laser
NCT00375765PHASE4COMPLETEDEffects On Dihydrotestosterone Regulated Gene Expression In Benign Prostatic Hyperplasia Or Prostate Cancer
NCT00379067PHASE4COMPLETEDA Phase 4 Study With Tamsulosin OCAS to Assess Nighttime Voiding.
NCT00421421PHASE4TERMINATEDEffects Of Dutasteride On Risk Reduction Of Acute Urinary Retention Relapse Following Trial Without Catheter
NCT00465101PHASE4COMPLETEDA Long-Term Study Examining the Treatment of Benign Prostatic Hyperplasia With Photoselective Vaporization
NCT00542165PHASE4COMPLETEDMulticenter Prospective Study on the Changes of Sexual Function Following Treatment With Alfuzosin (Xatral XL®) in Patients With Benign Prostate Hypertrophy
NCT00637715PHASE4COMPLETEDOnce Daily Given Alfuzosin in the Treatment of BPH
NCT00687388PHASE4WITHDRAWNThe Clinical Efficacy of Non-steroidal Anti-inflammation Drugs in Patients With Benign Prostatic Hyperplasia
NCT00690950PHASE4UNKNOWNA Study to Determine the Improvement of the Symptoms of Benign Prostatic Hyperplasia (BPH) When Switching Subjects From Proscar to Avodart
NCT00696761PHASE4COMPLETEDThe Long Term Effects of Alfuzosin(Xatral XL) in Lower Urinary Tract Symptoms(LUTS)/BPH Patients
NCT00701779PHASE4COMPLETEDDutasteride and Flex Dose of Tamsulosin on as Needed Basis, to Treat Benign Prostatic Hyperplasia
NCT00771394PHASE4COMPLETEDSolifenacin as Add-on Therapy for Overactive Bladder Symptoms in Men Treated for Benign Prostatic Hyperplasia
NCT00827814PHASE4COMPLETEDEffect of Dutasteride on Bladder Wall Hypertrophy in Patients With Benign Prostatic Obstruction
NCT00836823PHASE4COMPLETEDEvaluation of Symptom-specific Goal Achievement
NCT00880672PHASE4COMPLETEDEffect of Dutasteride on HIF-1alpha and VEGF in the Prostate
NCT00922506PHASE4COMPLETEDCombination Treatment With Doxazosin Plus TolterodineSR 2 mg Versus 4mg in Men With an Overactive Bladder (OAB) and Benign Prostatic Hyperplasia (BPH)
NCT00939120PHASE4COMPLETEDDutasteride With Tolterodine ER or Placebo to Treat Lower Urinary Tract Symptoms (LUTS)
NCT01259531PHASE4COMPLETEDStudy of a α1A Adrenoceptor Selective Antagonist Silodosin to Treat Severe Benign Prostatic Hyperplasia(BPH)
NCT01260129PHASE4COMPLETEDSafety and Efficacy of QD Versus BID Silodosin With Lower Urinary Tract Symptoms Suggestive of BPH
NCT01301599PHASE4COMPLETEDComparison Between Alpha Blocker Monotherapy and 5ARI Monotherapy Following Combination Therapy in Benign Prostatic Hyperplasia (BPH)
NCT01494337PHASE4COMPLETEDHolmium Laser Enucleation of Prostate(HOLEP) vs Greenlight(XPS) Laser Photoselective Vapo-Enucleation of Prostate(PVEP)
NCT01500057PHASE4COMPLETEDPhase 4 Study of Greenlight XPS Laser Versus BiVAP Saline Vaporization of the Prostate in Men With Symptomatic Benign Prostatic Hyperplasia
NCT01604811PHASE4COMPLETEDExploratory Study of L.S.E.S.r. (LipidoSterolic Extract of Serenoa Repens)(PERMIXON® 160 mg Hard Capsule) Versus Tamsulosine LP Activity on Inflammation Biomarkers in Urinary Symptoms Related to BPH (Benign Prostatic Hyperplasia)
NCT01631149PHASE4COMPLETEDEffect of Deep BLock on Intraoperative Surgical Conditions
NCT01675895PHASE4COMPLETEDAddition of Lidocaine to Levobupivacaine Reduces Intrathecal Block Duration
NCT01736033PHASE4UNKNOWNAdvanced Benefits of Alpha-blocker Monotherapy on Lower Urinary Tracts Symptoms(LUTS) Patients
NCT01747577PHASE4COMPLETEDPost Marketing Study to Evaluate the Efficacy and Safety of Solifenacin in Patients With OAB (Overactive Bladder) After TURP (Trans-urethral Resection of Prostate) or PVP (Photoselective Vaporization of Prostate)
NCT01757769PHASE4COMPLETEDEffectiveness and Safety of Silodosin in the Treatment of Benign Prostatic Hyperplasia
NCT01861041PHASE4UNKNOWNLow Dose Bupivacaine Spinal for Trans Uretral Prostatectomy.
NCT02006303PHASE4UNKNOWNProstatic Artery Embolization Versus 532 nm Green Light PVP for Catheterized Patients
NCT02021032PHASE4UNKNOWNPost-Marketing Study Using PROLIEVE® for the Treatment of Benign Prostatic Hyperplasia (BPH)
NCT02072499PHASE4COMPLETEDKTP Green Light Prostatectomy Compared With Open Prostatectomy

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
TAMSULOSIN495
ALFUZOSIN430
SOLIFENACIN427
DUTASTERIDE420
TADALAFIL416
SILODOSIN413
FINASTERIDE410
CETRORELIX44
CEPHALEXIN ANHYDROUS43
DOXAZOSIN43
MIRABEGRON43
TALAPORFIN SODIUM43
CIPROFLOXACIN42
ALCOHOL41
BUPIVACAINE41
CELECOXIB41
DEGARELIX41
DICLOFENAC SODIUM41
ETONOGESTREL41
FUROSEMIDE41
METHOXYFLURANE41
NITROFURANTOIN41
OXYGEN41
PACLITAXEL41
PYRIDOSTIGMINE41
RALOXIFENE41
FEXAPOTIDE310
TOPSALYSIN33
LONIDAMINE32
OZARELIX32