Hypogonadism

disease
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Also known as gonadotropin deficiencyhypogonadotropism

Summary

Hypogonadism (MONDO:0002146) is a disease (an umbrella term covering 6 Mondo subtypes) with 3 cohort genes (136 GWAS associations across 5 studies) and 197 clinical trials. Top therapeutic interventions include testosterone, testosterone undecanoate, and dutasteride.

At a glance

  • Umbrella term: 6 Mondo subtypes
  • Cohort genes: 3
  • GWAS associations: 136
  • ClinVar variants: 2
  • Clinical trials: 197

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical namehypogonadism
Mondo IDMONDO:0002146
MeSHD007006
DOIDDOID:1924
NCITC9227
SNOMED CT48130008
UMLSC0020619
MedGen5711
Is cancer (heuristic)no

Also known as: gonadotropin deficiency · hypogonadotropism

Data availability: 2 ClinVar variants · 136 GWAS associations (5 studies) · 1 GenCC gene-disease record · 4 cell lines.

Disease family

An umbrella term covering 6 Mondo subtypes.

Classification path: disease › human disease › disease by body system or component › reproductive system disordergonadal disorderhypogonadism

Related subtypes (5): precocious puberty, disorder of sexual differentiation, testicular disorder, ovarian disorder, gonadoblastoma

Subtypes (6): gonadal dysgenesis, eunuchism, hypogonadism, male, hypogonadotropic hypogonadism, Slti-Salem syndrome, weinstein kliman scully syndrome

Genetics & variants

GWAS landscape

136 GWAS associations across 5 studies. Top hits map to 25 distinct genes (as reported by GWAS).

Top associations by p-value

rsIDp-valueGeneRisk alleleOdds ratio
rs17999411e-136SHBGG0.24
rs1128005863e-119LINC03114 - NOLC1P1G0.15
rs1113868344e-96LINC03114 - NOLC1P1C0.15
rs108221601e-70JMJD1CG0.14
rs107617523e-55JMJD1CC0.14
rs28830913e-45RTL9G0.09
rs105215281e-38RTL9G0.09
rs561968601e-36FKBP4, ITFG2-AS1C0.31
rs12603264e-29GCKRT0.09
rs289294741e-25SERPINA1C0.33
rs7274289e-23SHBG - ATP1B2C0.18
rs7384096e-20PNPLA3G0.08
rs563328713e-19NR2F2-AS1C0.07
rs346662763e-15FLJ40194, ZNF652C0.07
rs283976634e-15FLJ40194C0.07
rs80615902e-14ATP2A1G0.06
rs59187646e-14ARA0.06
rs80235809e-14NR2F2-AS1C0.07
rs15533443331e-13SRD5A2 - LINC01946G0.17
rs585282652e-13ZNF652-AS1AGCCTG0.07
rs39767e-13SERPINF2G0.06
rs99868299e-13DGKB - GTF3AP5G0.06
rs116550561e-12FLJ40194C0.06
rs793918623e-12LINC02490 - WDR72C0.27
rs620334053e-12FTOC0.06
rs121506604e-12SHBGT0.26
rs41490562e-11SLCO1B1C0.08
rs2022007602e-11NR2F6G0.13
rs736321873e-11RNU6-394P - ARG0.07
rs64798974e-11JMJD1CT0.11

Top studies (by case count)

StudyLead authorYearCasesControlsTitle
GCST90503316Pagadala MS202500Discovery of novel ancestry specific genes for androgens and hypogonadism in Million Veteran Program Men.
GCST90503320Pagadala MS202500Discovery of novel ancestry specific genes for androgens and hypogonadism in Million Veteran Program Men.
GCST90503324Pagadala MS202500Discovery of novel ancestry specific genes for androgens and hypogonadism in Million Veteran Program Men.
GCST90503328Pagadala MS202500Discovery of novel ancestry specific genes for androgens and hypogonadism in Million Veteran Program Men.
GCST90570530Pagadala MS202500Discovery of novel ancestry specific genes for androgens and hypogonadism in Million Veteran Program Men.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

TierVariants
Tier 1: coding7
Tier 2: splice/UTR2
Tier 3: regulatory3
Tier 4: intronic/intergenic38

MAF distribution

BucketVariants
common (>=0.05)48
low_freq (0.01-0.05)0
rare (<0.01)0
unknown2

Functional consequences

ConsequenceCount
intron_variant26
intergenic_variant12
missense_variant7
regulatory_region_variant3
5_prime_UTR_variant1
3_prime_UTR_variant1

Top variants

rsIDChrPosAllelesMAFConsequenceGenep-valueTier
rs1799941177630105G>A,T0.055_prime_UTR_variantSHBG1e-136Tier 2: splice/UTR
rs112800586X8948222G>A,T0.05intergenic_variantLINC03114 - NOLC1P13e-119Tier 4: intronic/intergenic
rs111386834X8938654T>C0.05intergenic_variantLINC03114 - NOLC1P14e-96Tier 4: intronic/intergenic
rs108221601063353036T>A,G0.05intron_variantJMJD1C1e-70Tier 4: intronic/intergenic
rs107617521063400561T>C0.05intron_variantJMJD1C3e-55Tier 4: intronic/intergenic
rs2883091X110440911G>C0.05intron_variantRTL93e-45Tier 4: intronic/intergenic
rs10521528X110445924A>G0.05intron_variantRTL91e-38Tier 4: intronic/intergenic
rs56196860122799164C>A0.05missense_variantFKBP4, ITFG2-AS11e-36Tier 1: coding
rs1260326227508073T>A,C,G0.05missense_variantGCKR4e-29Tier 1: coding
rs289294741494378610C>A,G,T0.05missense_variantSERPINA11e-25Tier 1: coding
rs727428177634474T>A,C,G0.05regulatory_region_variantSHBG - ATP1B29e-23Tier 3: regulatory
rs7384092243928847C>A,G,T0.05missense_variantPNPLA36e-20Tier 1: coding
rs563328711596171587C>A,T0.05intron_variantNR2F2-AS13e-19Tier 4: intronic/intergenic
rs346662761749302124T>A,C,G0.05intron_variantFLJ40194, ZNF6523e-15Tier 4: intronic/intergenic
rs283976631749250821C>T0.05intron_variantFLJ401944e-15Tier 4: intronic/intergenic
rs80615901628883809A>C,G0.05intron_variantATP2A12e-14Tier 4: intronic/intergenic
rs5918764X67717865A>G,T0.05intron_variantAR6e-14Tier 4: intronic/intergenic
rs80235801596165062T>C0.05intron_variantNR2F2-AS19e-14Tier 4: intronic/intergenic
rs1553344333231764291GGAGTATGTTCTTGCTGAT>GA0.05regulatory_region_variantSRD5A2 - LINC019461e-13Tier 3: regulatory
rs585282651749367211A>AG,AGCCCG,AGCCTG,AGCTG0.05intron_variantZNF652-AS12e-13Tier 4: intronic/intergenic
rs3976171749797G>A,T0.05intron_variantSERPINF27e-13Tier 4: intronic/intergenic
rs9986829714979634G>A,C0.05intergenic_variantDGKB - GTF3AP59e-13Tier 4: intronic/intergenic
rs116550561749286745C>G,T0.05intron_variantFLJ401941e-12Tier 4: intronic/intergenic
rs793918621553447229A>Cintron_variantLINC02490 - WDR723e-12Tier 4: intronic/intergenic
rs620334051653788475C>T0.05intron_variantFTO3e-12Tier 4: intronic/intergenic
rs12150660177618597G>T0.05intron_variantSHBG4e-12Tier 4: intronic/intergenic
rs41490561221178615T>A,C0.05missense_variantSLCO1B12e-11Tier 1: coding
rs2022007601917236045G>C0.05missense_variantNR2F62e-11Tier 1: coding
rs73632187X67105003G>A0.05intergenic_variantRNU6-394P - AR3e-11Tier 4: intronic/intergenic
rs64798971063376868C>T0.05intron_variantJMJD1C4e-11Tier 4: intronic/intergenic

ClinVar germline variants

2 retrieved; paginated sample, class counts are floors:

1 pathogenic, 1 uncertain significance

ClinVarVariant (HGVS)GeneClassificationReview
1183968NM_152515.5(CKAP2L):c.1463_1467del (p.Thr488fs)CKAP2LPathogeniccriteria provided, single submitter
1676256NM_017563.5(IL17RD):c.1371T>G (p.Ile457Met)IL17RDUncertain significancecriteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 5 · Orphanet: 3 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

GeneClassificationInheritanceDiseaseRecords
SOHLH1LimitedAutosomal recessivehypogonadism5

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
SOHLH1Orphanet:399805Male infertility with azoospermia or oligozoospermia due to single gene mutation
IL17RDOrphanet:478Kallmann syndrome
CKAP2LOrphanet:3255Filippi syndrome

Cohort genes → proteins

3 cohort genes, 3 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence3

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
SOHLH1HGNC:27845ENSG00000165643Q5JUK2Spermatogenesis- and oogenesis-specific basic helix-loop-helix-containing protein 1gencc
IL17RDHGNC:17616ENSG00000144730Q8NFM7Interleukin-17 receptor Dclinvar
CKAP2LHGNC:26877ENSG00000169607Q8IYA6Cytoskeleton-associated protein 2-likeclinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
SOHLH1Spermatogenesis- and oogenesis-specific basic helix-loop-helix-containing protein 1Transcription regulator of both male and female germline differentiation.
IL17RDInterleukin-17 receptor DFeedback inhibitor of fibroblast growth factor mediated Ras-MAPK signaling and ERK activation.
CKAP2LCytoskeleton-associated protein 2-likeMicrotubule-associated protein required for mitotic spindle formation and cell-cycle progression in neural progenitor cells.

Protein-family classification

Druggable: 0 · Difficult: 1 · Unknown: 2 · Druggable fraction: 0.0

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 factor12.8×0.587
Other/Unknown21.2×0.587

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
SOHLH1Transcription factornobHLH_dom, HLH_DNA-bd_sf, TCFL5/SOLH1/2
IL17RDOther/UnknownnoSEFIR_dom, IL17R_D_N, Toll_tir_struct_dom_sf
CKAP2LOther/UnknownnoCKAP2_C, CKAP2-like

Expression context

Cohort genes with no expression data: 0.

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

Breadth distribution (Bgee present_calls)

BucketGenes
narrow (1-5 tissues)0
moderate (6-20)0
broad (>20)3
unknown0

Top tissues across cohort

TissueCohort genes
anterior cingulate cortex1
primordial germ cell in gonad1
right frontal lobe1
mammary duct1
oocyte1
secondary oocyte1
embryo1
ganglionic eminence1
ventricular zone1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
SOHLH170tissue_specificyesright frontal lobe, primordial germ cell in gonad, anterior cingulate cortex
IL17RD236broadyessecondary oocyte, oocyte, mammary duct
CKAP2L149ubiquitousmarkerventricular zone, ganglionic eminence, embryo

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

SymbolInteractor count
SOHLH11,483
IL17RD981
CKAP2L733

Structural data

PDB: 0 · AlphaFold-only: 3 · No structure: 0

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
IL17RDQ8NFM769.68
SOHLH1Q5JUK258.62
CKAP2LQ8IYA654.68

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 1. Enrichment computed across 3 evidence-associated genes (1 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 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
MAP2K and MAPK activation1285.5×0.004IL17RD

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 2 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
oocyte differentiation12106.5×0.002SOHLH1
negative regulation of epithelial to mesenchymal transition1205.5×0.012IL17RD
negative regulation of transforming growth factor beta receptor signaling pathway186.9×0.019IL17RD
spermatogenesis117.6×0.068SOHLH1
cell differentiation114.6×0.068SOHLH1

Therapeutics

Drugs indicated for this disease

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

DrugDevelopment status
Choriogonadotropin AlfaApproved (phase 4)
EstradiolApproved (phase 4)
Estradiol ValerateApproved (phase 4)
Estrogens, ConjugatedApproved (phase 4)
Estrogens, EsterifiedApproved (phase 4)
FluoxymesteroneApproved (phase 4)
FollitropinApproved (phase 4)
Follitropin AlfaApproved (phase 4)
Follitropin BetaApproved (phase 4)
MethyltestosteroneApproved (phase 4)
Norethindrone AcetateApproved (phase 4)
TestosteroneApproved (phase 4)
Testosterone CypionateApproved (phase 4)
Testosterone EnanthateApproved (phase 4)
Testosterone UndecanoateApproved (phase 4)
CholecalciferolPhase 3 (in late-stage trials)
Corifollitropin AlfaPhase 3 (in late-stage trials)
DutasteridePhase 3 (in late-stage trials)
Gonadotropin, ChorionicPhase 3 (in late-stage trials)
Insulin HumanPhase 3 (in late-stage trials)
LetrozolePhase 3 (in late-stage trials)
MenotropinsPhase 3 (in late-stage trials)

Earlier-phase candidates (phase 2, investigational — efficacy not yet established): Anastrozole, Clomiphene, Enclomiphene, KISSPEPTIN-10, Ketoconazole, Leuprolide, Lutropin Alfa, Naloxone.

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 3

Druggability breadth: 0 of 3 evidence-associated genes (0%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

SymbolMoleculesMax phase
SOHLH100
IL17RD00
CKAP2L00

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

Pharmacogenomics

Cohort genes with a PharmGKB record: 3; with CPIC/DPWG dosing guidelines: 0.

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

Chemical tractability of cohort targets

0 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.

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)0
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug3SOHLH1, IL17RD, CKAP2L

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
SOHLH10
IL17RD0
CKAP2L0

Clinical trials & evidence

Clinical trials

Clinical trials: 197.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified52
PHASE244
PHASE442
PHASE331
PHASE120
PHASE2/PHASE33
PHASE1/PHASE23
EARLY_PHASE12

Top trials by phase / activity

NCTPhaseStatusTitle
NCT06385509PHASE4ACTIVE_NOT_RECRUITINGA Phase 4 Study to Evaluate Adrenal Function in Hypogonadal Men Treated With JATENZO® for 12 Months
NCT06455969PHASE4RECRUITINGAdaptions and Resiliency to Multi-Stressor OpeRations
NCT00194675PHASE4COMPLETEDTRADE-Testosterone Replacement and Dutasteride Effectiveness
NCT00240981PHASE4TERMINATEDTOM: Testosterone in Older Men With Sarcopenia
NCT00287586PHASE4COMPLETEDTestosterone Replacement in Older Men and Atherosclerosis Progression
NCT00304213PHASE4WITHDRAWNDoes Testosterone Improve Function in Hypogonadal Older Men
NCT00349362PHASE4COMPLETEDTestosterone for Men With Insulin Treated Type 2 Diabetes
NCT00421460PHASE4COMPLETEDThe Therapy of Nebido as Mono or in Combination With PDE-5 Inhibitors in Hypogonadal Patients With Erectile Dysfunction
NCT00440440PHASE4WITHDRAWNEffect of Testosterone Gel Replacement on Fat Mass in Males With Low Testosterone Levels and Diabetes
NCT00487734PHASE4COMPLETEDEffect of Testosterone Replacement on Insulin Resistance
NCT00504712PHASE4COMPLETEDTestosterone for Peripheral Vascular Disease
NCT00700024PHASE4UNKNOWNOdense Androgen Study - The Effect of Testim and Training in Hypogonadal Men
NCT00710827PHASE4WITHDRAWNNebido Versus Placebo in Elderly Men With Typical Symptoms of Late Onset Hypogonadism Over a Period of 54 Weeks
NCT00752869PHASE4COMPLETEDEfficacy Study for Use of Dutasteride (Avodart) With Testosterone Replacement
NCT00837616PHASE4COMPLETEDEstrogen Dosing in Turner Syndrome: Pharmacology and Metabolism
NCT01084369PHASE4TERMINATEDEffect of Testosterone on Endothelial Function and Microcirculation in Type 2 Diabetic Patients With Hypogonadism
NCT01092858PHASE4TERMINATEDNEBIDO in Symptomatic Late Onset Hypogonadism (SLOH)
NCT01107067PHASE4COMPLETEDTestosterone Replacement Therapy Decreases Plasma Paraoxonase 1 Enzyme Activity In Male Patients With Hypogonadism
NCT01123278PHASE4COMPLETEDTestosterone Replacement in Metabolic Syndrome and Inflammation
NCT01127659PHASE4COMPLETEDTestosterone Replacement in Men With Diabetes and Obesity
NCT01160341PHASE4COMPLETEDMetabolic Syndrome Criteria and the Effect of Testosterone Treatment in Young Men With Hypogonadism
NCT01560546PHASE4COMPLETEDTestosterone Therapy of Men With Type 2 Diabetes Mellitus (T2DM)
NCT01689896PHASE4WITHDRAWNTestosterone and Pain Sensitivity
NCT01748370PHASE4COMPLETEDVitamin D Treatment and Hypogonadism in Men
NCT01893281PHASE4COMPLETEDThe Effect of Testosterone Topical Solution (LY900011) in Hypogonadal Men With Suboptimal Response to a Topical Testosterone Gel
NCT02102646PHASE4COMPLETEDMRI Substudy; Metabolic Changes Due to Iatrogenic Hypogonadism
NCT02111434PHASE4COMPLETEDVisceral Adiposity Index and Triglyceride/High-density Lipoprotein Cholesterol Ratio in the Congenital Hypogonadotropic Hypogonadism and Effect of Testosteron Treatment
NCT02111473PHASE4COMPLETEDThe Effect of Testosteron Replacement Treatment on the Fibroblast Growth Factor-23, Asymmetric Dimethylarginine and Vitamin D Levels in the Congenital Hypogonadotropic Hypogonadism
NCT02366975PHASE4COMPLETEDTRT on BPH Hypoganadal MetS Patients. Florence-PROTEST
NCT02433730PHASE4COMPLETEDTestosterone Therapy in Hypogonadal Men Treated With Opioids
NCT02937740PHASE4COMPLETEDOpen-Label Study, Evaluating Patient Satisfaction and Symptom Improvement When Treating Male Hypogonadism With Natesto™
NCT02959853PHASE4COMPLETEDAromatase Inhibitors and Weight Loss in Severely Obese Hypogonadal Male Veterans (Pilot)
NCT03057899PHASE4COMPLETEDEfficacy of Fenugreek Seed and Lespedeza Cuneata in TDS
NCT03126656PHASE4COMPLETEDEffects of Testosterone on Myocardial Repolarization
NCT03518034PHASE4COMPLETEDA Study to Evaluate the Effect of Testosterone Replacement Therapy (TRT) on the Incidence of Major Adverse Cardiovascular Events (MACE) and Efficacy Measures in Hypogonadal Men
NCT03619330PHASE4COMPLETEDTestosterone Replacement Therapy and Liraglutide Effects on Weight Loss in Hypogonadism.
NCT03887936PHASE4COMPLETEDTestosterone Therapy and Bone Quality in Men With Diabetes and Hypogonadism
NCT04274894PHASE4COMPLETEDA Study of the Effect of Topical Testosterone Replacement Therapy on Blood Pressure in Adult Male Participants With Hypogonadism
NCT04320745PHASE4COMPLETEDA Study to Evaluate Androderm®’s Effect on Blood Pressure in Adult Hypogonodal Male Participants
NCT04456296PHASE4COMPLETEDA Study of the Effect of Testosterone Replacement Therapy on Blood Pressure in Adult Male Participants With Hypogonadism

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
TESTOSTERONE450
TESTOSTERONE UNDECANOATE414
DUTASTERIDE47
ALENDRONIC ACID46
CLOMIPHENE43
GONADORELIN ACETATE43
TESTOSTERONE ENANTHATE43
FINASTERIDE42
GOSERELIN42
KETOCONAZOLE42
LEVOKETOCONAZOLE42
SODIUM CHLORIDE42
TESTOSTERONE CYPIONATE42
ANAKINRA41
ANASTROZOLE41
CORIFOLLITROPIN ALFA41
ESTRADIOL41
GONADOTROPIN, CHORIONIC41
LETROZOLE41
LIRAGLUTIDE41
PIOGLITAZONE41
TRIPTORELIN41
ENCLOMIPHENE33
ACYLINE24
FISPEMIFENE21
KISSPEPTIN21
STANOLONE21
CHEMBL4746472029
CHEMBL407338703
CHEMBL123325502