Hypogonadotropic hypogonadism 2 with or without anosmia

disease
On this page

Also known as FGFR1 hypogonadotropic hypogonadismHH2hypogonadotropic hypogonadism caused by mutation in FGFR1KAL2

Summary

Hypogonadotropic hypogonadism 2 with or without anosmia (MONDO:0007844) is a disease caused by FGFR1 (GenCC Definitive), with 5 cohort genes.

At a glance

  • Causal gene: FGFR1 (GenCC Definitive)
  • Cohort genes: 5
  • ClinVar variants: 964

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical namehypogonadotropic hypogonadism 2 with or without anosmia
Mondo IDMONDO:0007844
OMIM147950
DOIDDOID:0090083
UMLSC1563720
MedGen289648
GARD0003070
Is cancer (heuristic)no

Also known as: FGFR1 hypogonadotropic hypogonadism · HH2 · hypogonadotropic hypogonadism 2 with or without anosmia · hypogonadotropic hypogonadism caused by mutation in FGFR1 · KAL2

Data availability: 964 ClinVar variants · 4 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by body system or component › syndromic diseaseKallmann syndromehypogonadotropic hypogonadism 2 with or without anosmia

Related subtypes (17): hypogonadotropic hypogonadism 3 with or without anosmia, hypogonadotropic hypogonadism 1 with or without anosmia, hypogonadotropic hypogonadism 4 with or without anosmia, hypogonadotropic hypogonadism 5 with or without anosmia, hypogonadotropic hypogonadism 6 with or without anosmia, hypogonadotropic hypogonadism 8 with or without anosmia, hypogonadotropic hypogonadism 9 with or without anosmia, hypogonadotropic hypogonadism 11 with or without anosmia, hypogonadotropic hypogonadism 14 with or without anosmia, hypogonadotropic hypogonadism 15 with or without anosmia, hypogonadotropic hypogonadism 16 with or without anosmia, hypogonadotropic hypogonadism 17 with or without anosmia, hypogonadotropic hypogonadism 18 with or without anosmia, hypogonadotropic hypogonadism 19 with or without anosmia, hypogonadotropic hypogonadism 20 with or without anosmia, hypogonadotropic hypogonadism 21 with or without anosmia, hypogonadotropic hypogonadism 22 with or without anosmia

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

600 retrieved; paginated sample, class counts are floors:

228 uncertain significance, 192 likely benign, 71 pathogenic, 43 conflicting classifications of pathogenicity, 36 likely pathogenic, 15 pathogenic/likely pathogenic, 9 benign/likely benign, 5 benign, 1 risk factor

ClinVarVariant (HGVS)GeneClassificationReview
1455925NC_000008.10:g.(?37595441)(38961219_?)delEIF4EBP1Pathogeniccriteria provided, single submitter
1074220NM_023110.3(FGFR1):c.979_983del (p.His327fs)FGFR1Pathogeniccriteria provided, single submitter
1184446NM_023110.3(FGFR1):c.2122G>T (p.Glu708Ter)FGFR1Pathogeniccriteria provided, single submitter
1208776NM_023110.3(FGFR1):c.962_963del (p.Lys321fs)FGFR1Pathogeniccriteria provided, multiple submitters, no conflicts
132646NM_023110.3(FGFR1):c.790A>C (p.Asn264His)FGFR1Pathogenicno assertion criteria provided
132647NM_023110.3(FGFR1):c.1460G>A (p.Gly487Asp)FGFR1Pathogeniccriteria provided, single submitter
132648NM_023110.3(FGFR1):c.2084C>T (p.Thr695Ile)FGFR1Pathogenicno assertion criteria provided
1335817NM_023110.3(FGFR1):c.1981C>T (p.Arg661Ter)FGFR1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1341671NM_023110.3(FGFR1):c.748C>T (p.Arg250Trp)FGFR1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1341672NM_023110.3(FGFR1):c.1855-1G>AFGFR1Pathogenicno assertion criteria provided
1418780NM_023110.3(FGFR1):c.1265dup (p.Leu423fs)FGFR1Pathogeniccriteria provided, single submitter
16279NM_023110.3(FGFR1):c.755C>G (p.Pro252Arg)FGFR1Pathogeniccriteria provided, multiple submitters, no conflicts
16282NM_023110.3(FGFR1):c.1864C>T (p.Arg622Ter)FGFR1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
16290NM_023110.3(FGFR1):c.1141T>C (p.Cys381Arg)FGFR1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
16293NM_023110.3(FGFR1):c.2038C>T (p.Gln680Ter)FGFR1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
16296NM_023110.3(FGFR1):c.1825C>T (p.Arg609Ter)FGFR1Pathogeniccriteria provided, multiple submitters, no conflicts
16301NM_023110.3(FGFR1):c.2292G>T (p.Gln764His)FGFR1Pathogenicno assertion criteria provided
16303NM_023110.3(FGFR1):c.749G>A (p.Arg250Gln)FGFR1Pathogeniccriteria provided, multiple submitters, no conflicts
1709350NM_023110.3(FGFR1):c.1969dup (p.Thr657fs)FGFR1Pathogeniccriteria provided, single submitter
1801171NM_023110.3(FGFR1):c.246_247del (p.Glu84fs)FGFR1Pathogeniccriteria provided, multiple submitters, no conflicts
180153NM_023110.3(FGFR1):c.1916T>C (p.Ile639Thr)FGFR1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
180154NM_023110.3(FGFR1):c.1037_1038del (p.Ser346fs)FGFR1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
180156NM_023110.3(FGFR1):c.296A>G (p.Tyr99Cys)FGFR1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
180160NM_023110.3(FGFR1):c.2059G>A (p.Gly687Arg)FGFR1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1997422NM_023110.3(FGFR1):c.111del (p.Val38fs)FGFR1Pathogeniccriteria provided, single submitter
2011123NM_023110.3(FGFR1):c.625del (p.Arg209fs)FGFR1Pathogeniccriteria provided, single submitter
2029325NM_023110.3(FGFR1):c.780del (p.Leu261fs)FGFR1Pathogeniccriteria provided, single submitter
2097346NM_023110.3(FGFR1):c.1568_1569dup (p.Asp524fs)FGFR1Pathogeniccriteria provided, single submitter
2105298NM_023110.3(FGFR1):c.2048T>G (p.Val683Gly)FGFR1Pathogeniccriteria provided, single submitter
2136660NM_023110.3(FGFR1):c.1883A>G (p.Asn628Ser)FGFR1Pathogeniccriteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 36 · Orphanet: 21 · 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
FGFR1DefinitiveAutosomal dominanthypogonadotropic hypogonadism 2 with or without anosmia36

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
FGFR1Orphanet:168953Myeloid/lymphoid neoplasm associated with FGFR1 rearrangement
FGFR1Orphanet:2117Hartsfield syndrome
FGFR1Orphanet:220386Semilobar holoprosencephaly
FGFR1Orphanet:2396Encephalocraniocutaneous lipomatosis
FGFR1Orphanet:251576Gliosarcoma
FGFR1Orphanet:251579Giant cell glioblastoma
FGFR1Orphanet:251615Pilomyxoid astrocytoma
FGFR1Orphanet:2645Osteoglosphonic dysplasia
FGFR1Orphanet:280200Microform holoprosencephaly
FGFR1Orphanet:314950Primary hypereosinophilic syndrome
FGFR1Orphanet:3157Septo-optic dysplasia spectrum
FGFR1Orphanet:3366Non-syndromic metopic craniosynostosis
FGFR1Orphanet:432Normosmic congenital hypogonadotropic hypogonadism
FGFR1Orphanet:478Kallmann syndrome
FGFR1Orphanet:93258Pfeiffer syndrome type 1
FGFR1Orphanet:93924Lobar holoprosencephaly
FGFR1Orphanet:99798Oligodontia
PROKR2Orphanet:3157Septo-optic dysplasia spectrum
PROKR2Orphanet:432Normosmic congenital hypogonadotropic hypogonadism
PROKR2Orphanet:478Kallmann syndrome
PROKR2Orphanet:95496Pituitary stalk interruption syndrome

Cohort genes → proteins

5 cohort genes, 5 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence5

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
FGFR1HGNC:3688ENSG00000077782P11362Fibroblast growth factor receptor 1gencc,clinvar
PROKR2HGNC:15836ENSG00000101292Q8NFJ6Prokineticin receptor 2clinvar
ADGRA2HGNC:17849ENSG00000020181Q96PE1Adhesion G protein-coupled receptor A2clinvar
GOT1L1HGNC:28487ENSG00000169154Q8NHS2Putative aspartate aminotransferase, cytoplasmic 2clinvar
EIF4EBP1HGNC:3288ENSG00000187840Q13541Eukaryotic translation initiation factor 4E-binding protein 1clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
FGFR1Fibroblast growth factor receptor 1Tyrosine-protein kinase that acts as a cell-surface receptor for fibroblast growth factors and plays an essential role in the regulation of embryonic development, cell proliferation, differentiation and migration.
PROKR2Prokineticin receptor 2Receptor for prokineticin 2.
ADGRA2Adhesion G protein-coupled receptor A2Endothelial receptor which functions together with RECK to enable brain endothelial cells to selectively respond to Wnt7 signals (WNT7A or WNT7B).
EIF4EBP1Eukaryotic translation initiation factor 4E-binding protein 1Repressor of translation initiation that regulates EIF4E activity by preventing its assembly into the eIF4F complex: hypophosphorylated form competes with EIF4G1/EIF4G3 and strongly binds to EIF4E, leading to repress translation.

Protein-family classification

Druggable: 4 · Difficult: 0 · Unknown: 1 · Druggable fraction: 0.8

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
GPCR29.6×0.064
Kinase15.5×0.336
Enzyme (other)12.4×0.471
Other/Unknown10.4×0.983

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
FGFR1Kinaseyes2.7.10.1Prot_kinase_dom, Ser-Thr/Tyr_kinase_cat_dom, Ig_sub2
PROKR2GPCRyesGPCR_Rhodpsn, NPY_rcpt, GPCR_Rhodpsn_7TM
ADGRA2GPCRyesGPS, Cys-rich_flank_reg_C, GPCR_2_secretin-like
GOT1L1Enzyme (other)yes2.6.1.1Asp_trans, Aminotransferase_I/II_large, PyrdxlP-dep_Trfase_major
EIF4EBP1Other/UnknownnoEIF4EBP

Expression context

Cohort genes with no expression data: 0.

4 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)0
broad (>20)5
unknown0

Top tissues across cohort

TissueCohort genes
stromal cell of endometrium2
buccal mucosa cell1
calcaneal tendon1
cortical plate1
ganglionic eminence1
ventricular zone1
endocervix1
seminal vesicle1
left testis1
male germ line stem cell (sensu Vertebrata) in testis1
testis1
body of pancreas1
lower esophagus mucosa1
parotid gland1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
FGFR1292ubiquitousmarkerbuccal mucosa cell, stromal cell of endometrium, calcaneal tendon
PROKR232tissue_specificyescortical plate, ganglionic eminence, ventricular zone
ADGRA2226ubiquitousmarkerstromal cell of endometrium, seminal vesicle, endocervix
GOT1L142tissue_specificmarkermale germ line stem cell (sensu Vertebrata) in testis, left testis, testis
EIF4EBP1251ubiquitousmarkerbody of pancreas, parotid gland, lower esophagus mucosa

Protein interactions among cohort

Intra-cohort edges: 1.

Hub genes (top 10 by interactor count)

SymbolInteractor count
FGFR15,693
EIF4EBP12,189
GOT1L11,699
ADGRA21,345
PROKR2844

Intra-cohort edges

ABSources
FGFR1PROKR2string_interaction

Structural data

PDB: 2 · AlphaFold-only: 3 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
FGFR1P1136283
EIF4EBP1Q1354124

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
GOT1L1Q8NHS291.97
PROKR2Q8NFJ678.50
ADGRA2Q96PE170.47

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 32. Enrichment computed across 5 evidence-associated genes (3 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 3 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Signaling by FGFR1 amplification mutants11903.3×0.011FGFR1
FGFR1c and Klotho ligand binding and activation1951.7×0.011FGFR1
Signaling by plasma membrane FGFR1 fusions1951.7×0.011FGFR1
Epithelial-Mesenchymal Transition (EMT) during gastrulation1475.8×0.015FGFR1
FGFR1b ligand binding and activation1423.0×0.015FGFR1
Signaling by activated point mutants of FGFR11317.2×0.015FGFR1
FGFR1c ligand binding and activation1253.8×0.015FGFR1
Phospholipase C-mediated cascade: FGFR11223.9×0.015FGFR1
Downstream signaling of activated FGFR11181.3×0.015FGFR1
Signal transduction by L11173.0×0.015FGFR1
PI-3K cascade:FGFR11173.0×0.015FGFR1
SHC-mediated cascade:FGFR11165.5×0.015FGFR1
mTORC1-mediated signalling1158.6×0.015EIF4EBP1
FRS-mediated FGFR1 signaling1152.3×0.015FGFR1
Formation of paraxial mesoderm1135.9×0.016FGFR1
Negative regulation of FGFR1 signaling1122.8×0.016FGFR1
Eukaryotic Translation Initiation1102.9×0.016EIF4EBP1
Cap-dependent Translation Initiation1102.9×0.016EIF4EBP1
Signaling by FGFR1 in disease197.6×0.016FGFR1
PI3K Cascade190.6×0.016FGFR1
NCAM signaling for neurite out-growth190.6×0.016FGFR1
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S190.6×0.016EIF4EBP1
MTOR signalling188.5×0.016EIF4EBP1
Constitutive Signaling by Aberrant PI3K in Cancer142.3×0.031FGFR1
PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling132.3×0.039FGFR1
Peptide ligand-binding receptors124.7×0.049PROKR2
PIP3 activates AKT signaling122.3×0.052FGFR1
Translation120.7×0.053EIF4EBP1
RAF/MAP kinase cascade120.4×0.053FGFR1
G alpha (q) signalling events119.1×0.055PROKR2

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 5 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
vitamin D3 metabolic process11685.2×0.009FGFR1
regulation of establishment of blood-brain barrier11685.2×0.009ADGRA2
positive regulation of mitotic cell cycle DNA replication11685.2×0.009FGFR1
positive regulation of parathyroid hormone secretion11685.2×0.009FGFR1
regulation of extrinsic apoptotic signaling pathway in absence of ligand11685.2×0.009FGFR1
L-aspartate biosynthetic process11123.5×0.009GOT1L1
regulation of phosphate transport11123.5×0.009FGFR1
fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development11123.5×0.009FGFR1
regulation of lateral mesodermal cell fate specification11123.5×0.009FGFR1
ventricular zone neuroblast division1842.6×0.009FGFR1
negative regulation of fibroblast growth factor production1842.6×0.009FGFR1
positive regulation of phospholipase activity1674.1×0.009FGFR1
regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling1674.1×0.009FGFR1
diphosphate metabolic process1674.1×0.009FGFR1
chordate embryonic development1561.7×0.009FGFR1
regulation of chemotaxis1561.7×0.009ADGRA2
positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway1561.7×0.009FGFR1
cementum mineralization1481.5×0.010FGFR1
auditory receptor cell development1374.5×0.012FGFR1
paraxial mesoderm development1337.0×0.012FGFR1
lung-associated mesenchyme development1337.0×0.012FGFR1
response to sodium phosphate1337.0×0.012FGFR1
outer ear morphogenesis1306.4×0.012FGFR1
branching involved in salivary gland morphogenesis1280.9×0.013FGFR1
negative regulation of vascular endothelial growth factor signaling pathway1259.3×0.014ADGRA2
organ induction1240.7×0.014FGFR1
mesenchymal cell proliferation1224.7×0.014FGFR1
positive regulation of endothelial cell chemotaxis1198.3×0.016FGFR1
cell projection assembly1187.2×0.016FGFR1
negative regulation of translational initiation1177.4×0.016EIF4EBP1

Therapeutics

Drug target analysis

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

Druggability breadth: 4 of 5 evidence-associated genes (80%) 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
FGFR1PONATINIB

Top cohort targets by molecule count

SymbolMoleculesMax phase
FGFR1934
PROKR200
ADGRA200
GOT1L100
EIF4EBP100

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
PONATINIB4FGFR1
PEMIGATINIB4FGFR1
NINTEDANIB4FGFR1
FEDRATINIB4FGFR1
TIVOZANIB4FGFR1
LENVATINIB4FGFR1
AXITINIB4FGFR1
SORAFENIB4FGFR1
NICLOSAMIDE4FGFR1
INFIGRATINIB PHOSPHATE4FGFR1
INFIGRATINIB4FGFR1
REGORAFENIB4FGFR1
ENTRECTINIB4FGFR1
CABOZANTINIB4FGFR1
CAPIVASERTIB4FGFR1
VANDETANIB4FGFR1
NINTEDANIB ESYLATE4FGFR1
BRIGATINIB4FGFR1
ERDAFITINIB4FGFR1
UPADACITINIB4FGFR1
FUTIBATINIB4FGFR1
PAZOPANIB4FGFR1
SUNITINIB4FGFR1
DASATINIB4FGFR1
MIDOSTAURIN4FGFR1
LINIFANIB3FGFR1
SEMAXANIB3FGFR1
OLVEREMBATINIB3FGFR1
BRIVANIB ALANINATE3FGFR1
ORANTINIB3FGFR1

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 2.

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

SymbolAssaysType breakdown
FGFR11,465Binding:1428, Functional:24, ADMET:13
EIF4EBP133Binding:33
PROKR29Functional:5, Binding:4
ADGRA22Binding:2

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
FGFR12.7.10.1receptor protein-tyrosine kinase
GOT1L12.6.1.1aspartate transaminase

Cohort genes with high screening signal

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

SymbolChEMBL assays
FGFR11,465

Pharmacogenomics

Cohort genes with a PharmGKB record: 5; 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)
PONATINIB4FGFR1
PEMIGATINIB4FGFR1
NINTEDANIB4FGFR1
FEDRATINIB4FGFR1
TIVOZANIB4FGFR1
LENVATINIB4FGFR1
AXITINIB4FGFR1
SORAFENIB4FGFR1
NICLOSAMIDE4FGFR1
INFIGRATINIB PHOSPHATE4FGFR1
INFIGRATINIB4FGFR1
REGORAFENIB4FGFR1
ENTRECTINIB4FGFR1
CABOZANTINIB4FGFR1
CAPIVASERTIB4FGFR1
VANDETANIB4FGFR1
NINTEDANIB ESYLATE4FGFR1
BRIGATINIB4FGFR1
ERDAFITINIB4FGFR1
UPADACITINIB4FGFR1
FUTIBATINIB4FGFR1
PAZOPANIB4FGFR1
SUNITINIB4FGFR1
DASATINIB4FGFR1
MIDOSTAURIN4FGFR1
LINIFANIB3FGFR1
SEMAXANIB3FGFR1
OLVEREMBATINIB3FGFR1
BRIVANIB ALANINATE3FGFR1
ORANTINIB3FGFR1

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)1FGFR1
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug3PROKR2, ADGRA2, GOT1L1
EDifficult family or no structure, no drug1EIF4EBP1

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
PROKR29
ADGRA22
GOT1L10
EIF4EBP133

Clinical trials & evidence

Clinical trials

Clinical trials: 0.