glaucoma 3A

disease
On this page

Also known as buphthalmosglaucoma 3, primary congenital, Aglaucoma 3, primary congenital, type aglaucoma 3A, primary open angle, congenital, juvenile, or adult onsetGLC3APrimary Congenital glaucoma 3A

Summary

glaucoma 3A (MONDO:0009277) is a disease caused by CYP1B1 (GenCC Definitive), with 5 cohort genes.

At a glance

  • Prevalence: 1-9 / 100 000 (Europe) [Orphanet-validated]
  • Causal gene: CYP1B1 (GenCC Definitive)
  • Cohort genes: 5
  • ClinVar variants: 196
  • Phenotypes (HPO): 19

Clinical features

Epidemiology

Prevalence records

18 prevalence record(s), Orphanet:

TypeClassValueGeographyValidation
Prevalence at birth1-9 / 100 0002.2EuropeValidated
Prevalence at birth1-9 / 100 0002.9BelgiumValidated
Prevalence at birth1-9 / 100 0006.6FranceValidated
Prevalence at birth1-9 / 100 0002.8MaltaValidated
Prevalence at birth1-9 / 100 0003.6ItalyValidated
Prevalence at birth1-9 / 100 0005.6NetherlandsValidated
Prevalence at birth1-9 / 1 000 0000.8NorwayValidated
Prevalence at birth1-9 / 1 000 0000.9PortugalValidated
Prevalence at birth1-9 / 100 0006.5SpainValidated
Prevalence at birth1-9 / 100 0002.2United KingdomValidated
Prevalence at birth1-9 / 100 0003UkraineValidated
Prevalence at birth1-9 / 100 0001.5SwitzerlandValidated
Prevalence at birth1-9 / 100 0001.4PolandValidated
Prevalence at birth1-9 / 100 0004.1IrelandValidated
Prevalence at birth1-9 / 100 0004.1GermanyValidated
Prevalence at birth1-9 / 100 0002.8CroatiaValidated
Prevalence at birth1-9 / 100 0003.4AustriaValidated
Point prevalence1-9 / 100 000EuropeNot yet validated

Signs & symptoms

Clinical features (HPO)

19 HPO clinical features (Orphanet curated; top 19 by frequency):

HPO IDTermFrequency
HP:0000501GlaucomaVery frequent (80-99%)
HP:0012040Corneal stromal edemaVery frequent (80-99%)
HP:0000485MegalocorneaFrequent (30-79%)
HP:0000557BuphthalmosFrequent (30-79%)
HP:0000613PhotophobiaFrequent (30-79%)
HP:0000643BlepharospasmFrequent (30-79%)
HP:0001089Iris atrophyFrequent (30-79%)
HP:0007765Deep anterior chamberFrequent (30-79%)
HP:0007906Ocular hypertensionFrequent (30-79%)
HP:0007957Corneal opacityFrequent (30-79%)
HP:0009926EpiphoraFrequent (30-79%)
HP:0011490Abnormal Descemet membrane morphologyFrequent (30-79%)
HP:0025751Reduced anterior scleral thicknessFrequent (30-79%)
HP:0000545MyopiaOccasional (5-29%)
HP:0000572Visual lossOccasional (5-29%)
HP:0000646AmblyopiaOccasional (5-29%)
HP:0007663Reduced visual acuityOccasional (5-29%)
HP:0012803AnisometropiaOccasional (5-29%)
HP:0100693IridodonesisOccasional (5-29%)

Identifiers

Disease identifiers

FieldValue
Canonical nameglaucoma 3A
Mondo IDMONDO:0009277
OMIM231300
Orphanet98976
DOIDDOID:11211
NCITC148260
UMLSC1856439
MedGen383912
GARD0018224
Is cancer (heuristic)no

Also known as: buphthalmos · glaucoma 3, primary congenital, A · glaucoma 3, primary congenital, type a · glaucoma 3A, primary open angle, congenital, juvenile, or adult onset · GLC3A · Primary Congenital glaucoma 3A

Data availability: 196 ClinVar variants · 3 GenCC gene-disease records · 1 cell line.

Disease family

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary diseasehereditary glaucomacongenital glaucomaprimary congenital glaucomaCYP1B1-related glaucoma with or without anterior segment dysgenesisglaucoma 3A

Related subtypes (1): anterior segment dysgenesis 6

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

196 retrieved; paginated sample, class counts are floors:

87 uncertain significance, 31 pathogenic, 30 likely pathogenic, 19 conflicting classifications of pathogenicity, 13 benign, 7 likely benign, 6 pathogenic/likely pathogenic, 2 benign/likely benign, 1 not provided

ClinVarVariant (HGVS)GeneClassificationReview
2628067NM_015692.5(CPAMD8):c.3798_3861+1759delCPAMD8Pathogeniccriteria provided, single submitter
1076484NM_000104.4(CYP1B1):c.840C>A (p.Cys280Ter)CYP1B1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1120045NM_000104.4(CYP1B1):c.434_443del (p.Arg145fs)CYP1B1Pathogenicreviewed by expert panel
1254629NM_000104.4(CYP1B1):c.1310C>T (p.Pro437Leu)CYP1B1Pathogenicreviewed by expert panel
1322184NM_000104.4(CYP1B1):c.517G>T (p.Glu173Ter)CYP1B1Pathogenicreviewed by expert panel
1339135NM_000104.4(CYP1B1):c.1044-2A>GCYP1B1Pathogenicreviewed by expert panel
1339668NM_000104.4(CYP1B1):c.1090G>A (p.Val364Met)CYP1B1Pathogenicreviewed by expert panel
1442930NM_000104.4(CYP1B1):c.55C>T (p.Gln19Ter)CYP1B1Pathogeniccriteria provided, multiple submitters, no conflicts
2203048NM_000104.4(CYP1B1):c.1168C>A (p.Arg390Ser)CYP1B1Pathogenicreviewed by expert panel
2577219NM_000104.4(CYP1B1):c.317C>A (p.Ala106Asp)CYP1B1Pathogenicreviewed by expert panel
265390NM_000104.4(CYP1B1):c.830del (p.Phe276_Leu277insTer)CYP1B1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2681130NM_000104.4(CYP1B1):c.872A>G (p.Asp291Gly)CYP1B1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2681138NM_000104.4(CYP1B1):c.1140dup (p.Val381fs)CYP1B1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2687741NM_000104.4(CYP1B1):c.9del (p.Ser4fs)CYP1B1Pathogenicno assertion criteria provided
2734165NM_000104.4(CYP1B1):c.243C>G (p.Tyr81Ter)CYP1B1Pathogeniccriteria provided, multiple submitters, no conflicts
282564NM_000104.4(CYP1B1):c.1064_1076del (p.Arg355fs)CYP1B1Pathogenicreviewed by expert panel
3236111NM_000104.4(CYP1B1):c.83C>A (p.Ser28Ter)CYP1B1Pathogeniccriteria provided, single submitter
3236697NM_000104.4(CYP1B1):c.1333T>A (p.Phe445Ile)CYP1B1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
335952NM_000104.4(CYP1B1):c.1168C>T (p.Arg390Cys)CYP1B1Pathogenicreviewed by expert panel
3777763NC_000002.12:g.38012214_38131522delCYP1B1Pathogenicreviewed by expert panel
417858NM_000104.4(CYP1B1):c.1063_1075del (p.Arg355fs)CYP1B1Pathogenicno assertion criteria provided
523943NM_000104.4(CYP1B1):c.535del (p.Ala179fs)CYP1B1Pathogenicreviewed by expert panel
592512NM_000104.4(CYP1B1):c.1169G>A (p.Arg390His)CYP1B1Pathogenicreviewed by expert panel
68466NM_000104.4(CYP1B1):c.1200_1209dup (p.Thr404fs)CYP1B1Pathogenicreviewed by expert panel
68468NM_000104.4(CYP1B1):c.868dup (p.Arg290fs)CYP1B1Pathogenicreviewed by expert panel
7730NM_000104.4(CYP1B1):c.182G>A (p.Gly61Glu)CYP1B1Pathogenicreviewed by expert panel
7733NM_000104.4(CYP1B1):c.1405C>T (p.Arg469Trp)CYP1B1Pathogenicreviewed by expert panel
7735NM_000104.4(CYP1B1):c.1159G>A (p.Glu387Lys)CYP1B1Pathogenicreviewed by expert panel
7737NM_000104.4(CYP1B1):c.171G>A (p.Trp57Ter)CYP1B1Pathogenicreviewed by expert panel
7742NM_000104.4(CYP1B1):c.174del (p.Pro58_Leu59insTer)CYP1B1Pathogenicno assertion criteria provided

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 6 · Orphanet: 12 · 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
CYP1B1DefinitiveAutosomal recessiveCYP1B1-related glaucoma with or without anterior segment dysgenesis6

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
CYP1B1Orphanet:708Peters anomaly
CYP1B1Orphanet:98976Congenital glaucoma
CYP1B1Orphanet:98977Juvenile glaucoma
PXDNOrphanet:289499Congenital cataract microcornea with corneal opacity
PXDNOrphanet:6998502p25.3 microduplication syndrome
CPAMD8Orphanet:519388Autosomal recessive anterior segment dysgenesis
LTBP2Orphanet:238763Glaucoma secondary to spherophakia/ectopia lentis and megalocornea
LTBP2Orphanet:3449Weill-Marchesani syndrome
LTBP2Orphanet:98976Congenital glaucoma
LTBP3Orphanet:2623Geleophysic dysplasia
LTBP3Orphanet:2899Brachyolmia-amelogenesis imperfecta syndrome
LTBP3Orphanet:969Acromicric dysplasia

Cohort genes → proteins

5 cohort genes, 5 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence5

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
CYP1B1HGNC:2597ENSG00000138061Q16678Cytochrome P450 1B1gencc,clinvar
PXDNHGNC:14966ENSG00000130508Q92626Peroxidasin homologclinvar
CPAMD8HGNC:23228ENSG00000160111Q8IZJ3C3 and PZP-like alpha-2-macroglobulin domain-containing protein 8clinvar
LTBP2HGNC:6715ENSG00000119681Q14767Latent-transforming growth factor beta-binding protein 2clinvar
LTBP3HGNC:6716ENSG00000168056Q9NS15Latent-transforming growth factor beta-binding protein 3clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
CYP1B1Cytochrome P450 1B1A cytochrome P450 monooxygenase involved in the metabolism of various endogenous substrates, including fatty acids, steroid hormones and vitamins.
PXDNPeroxidasin homologCatalyzes the two-electron oxidation of bromide by hydrogen peroxide and generates hypobromite as a reactive intermediate which mediates the formation of sulfilimine cross-links between methionine and hydroxylysine residues within an uncro…
LTBP2Latent-transforming growth factor beta-binding protein 2May play an integral structural role in elastic-fiber architectural organization and/or assembly.
LTBP3Latent-transforming growth factor beta-binding protein 3Key regulator of transforming growth factor beta (TGFB1, TGFB2 and TGFB3) that controls TGF-beta activation by maintaining it in a latent state during storage in extracellular space.

Protein-family classification

Druggable: 2 · Difficult: 0 · Unknown: 3 · Druggable fraction: 0.4

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
Complement153.6×0.056
Antibody/Immunoglobulin15.8×0.240
Other/Unknown31.1×0.608

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
CYP1B1Other/UnknownnoCyt_P450, Cyt_P450_E_grp-I, Cyt_P450_CS
PXDNAntibody/Immunoglobulinyes1.11.1.7Cys-rich_flank_reg_C, VWF_dom, Leu-rich_rpt
CPAMD8ComplementyesMacroglobln_a2, Kazal_dom, MG2
LTBP2Other/UnknownnoEGF-type_Asp/Asn_hydroxyl_site, EGF, EGF-like_Ca-bd_dom
LTBP3Other/UnknownnoEGF-type_Asp/Asn_hydroxyl_site, EGF, EGF-like_Ca-bd_dom

Expression context

Cohort genes with no expression data: 0.

5 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
ascending aorta2
descending thoracic aorta2
thoracic aorta2
cartilage tissue1
pericardium1
synovial joint1
hair follicle1
stromal cell of endometrium1
tendon of biceps brachii1
apex of heart1
pancreatic ductal cell1
right lung1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
CYP1B1285ubiquitousmarkerpericardium, cartilage tissue, synovial joint
PXDN265ubiquitousmarkerstromal cell of endometrium, hair follicle, tendon of biceps brachii
CPAMD8227broadmarkerapex of heart, pancreatic ductal cell, right lung
LTBP2276ubiquitousmarkerdescending thoracic aorta, thoracic aorta, ascending aorta
LTBP3279broadmarkerdescending thoracic aorta, thoracic aorta, ascending aorta

Protein interactions among cohort

Intra-cohort edges: 3.

Hub genes (top 10 by interactor count)

SymbolInteractor count
PXDN9,915
CYP1B12,883
LTBP22,658
LTBP32,339
CPAMD8692

Intra-cohort edges

ABSources
CPAMD8LTBP2string_interaction
CPAMD8LTBP3string_interaction
CYP1B1LTBP2string_interaction

Structural data

PDB: 1 · AlphaFold-only: 4 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
CYP1B1Q166782

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
PXDNQ9262680.43
CPAMD8Q8IZJ372.99
LTBP3Q9NS1564.21
LTBP2Q1476758.33

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 13. Enrichment computed across 5 evidence-associated genes (4 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 4 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Elastic fibre formation2167.9×3e-04LTBP2, LTBP3
TGF-beta receptor signaling activates SMADs2163.1×3e-04LTBP2, LTBP3
Molecules associated with elastic fibres2154.3×3e-04LTBP2, LTBP3
Signaling by TGF-beta Receptor Complex2100.2×5e-04LTBP2, LTBP3
Defective CYP1B1 causes Glaucoma12855.0×9e-04CYP1B1
Signaling by TGFB family members257.7×1e-03LTBP2, LTBP3
Extracellular matrix organization231.6×0.003LTBP2, LTBP3
Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET)1356.9×0.005CYP1B1
Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE)1317.2×0.005CYP1B1
Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition1219.6×0.006PXDN
Crosslinking of collagen fibrils1142.8×0.008PXDN
Endogenous sterols198.5×0.011CYP1B1
Signal Transduction25.1×0.051LTBP2, LTBP3

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
eye development2140.4×0.005PXDN, CPAMD8
benzene-containing compound metabolic process13370.4×0.006CYP1B1
collagen fibril organization289.9×0.006CYP1B1, PXDN
transforming growth factor beta receptor signaling pathway263.6×0.006LTBP2, LTBP3
trabecular meshwork development11685.2×0.007CYP1B1
obsolete membrane lipid catabolic process1842.6×0.010CYP1B1
endothelial cell-cell adhesion1842.6×0.010CYP1B1
steroid catabolic process1481.5×0.010CYP1B1
retinal blood vessel morphogenesis1481.5×0.010CYP1B1
positive regulation of mesenchymal stem cell differentiation1481.5×0.010LTBP3
toxin metabolic process1421.3×0.010CYP1B1
lung saccule development1421.3×0.010LTBP3
positive regulation of mesenchymal stem cell proliferation1421.3×0.010LTBP3
angiogenesis225.0×0.010CYP1B1, PXDN
basement membrane assembly1374.5×0.010PXDN
omega-hydroxylase P450 pathway1306.4×0.012CYP1B1
blood vessel endothelial cell migration1280.9×0.012CYP1B1
negative regulation of cell adhesion mediated by integrin1259.3×0.013CYP1B1
supramolecular fiber organization1210.7×0.013LTBP2
positive regulation of bone resorption1198.3×0.013LTBP3
protein homotrimerization1198.3×0.013PXDN
negative regulation of bone mineralization1187.2×0.013LTBP3
retinal metabolic process1187.2×0.013CYP1B1
bone remodeling1187.2×0.013LTBP3
epoxygenase P450 pathway1177.4×0.013CYP1B1
intrinsic apoptotic signaling pathway in response to oxidative stress1168.5×0.013CYP1B1
sterol metabolic process1168.5×0.013CYP1B1
blood vessel morphogenesis1160.5×0.013CYP1B1
regulation of reactive oxygen species metabolic process1146.5×0.013CYP1B1
nitric oxide biosynthetic process1140.4×0.013CYP1B1

Therapeutics

Drug target analysis

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

Druggability breadth: 1 of 5 evidence-associated genes (20%) 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
CYP1B1PAZOPANIB

Top cohort targets by molecule count

SymbolMoleculesMax phase
CYP1B1224
PXDN00
CPAMD800
LTBP200
LTBP300

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
PAZOPANIB4CYP1B1
INDACATEROL4CYP1B1
ESTRADIOL4CYP1B1
CANNABIDIOL4CYP1B1
BERBERINE4CYP1B1
MELATONIN4CYP1B1
ERYTHROMYCIN4CYP1B1
CARVEDILOL4CYP1B1
RESVERATROL3CYP1B1
BERGAPTEN3CYP1B1
QUERCETIN3CYP1B1
CANNABINOL3CYP1B1
LUTEOLIN2CYP1B1
FORMONONETIN2CYP1B1
FLAVONE2CYP1B1
2-METHOXYESTRADIOL2CYP1B1
PINOCEMBRIN2CYP1B1
KHELLIN2CYP1B1
BAICALEIN2CYP1B1
PTEROSTILBENE2CYP1B1
KAEMPFEROL1CYP1B1
PLUMBAGIN1CYP1B1

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

SymbolAssaysType breakdown
CYP1B1408ADMET:281, Binding:127

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
PXDN1.11.1.7peroxidase

Cohort genes with high screening signal

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

SymbolChEMBL assays
CYP1B1408

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

22 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)
PAZOPANIB4CYP1B1
INDACATEROL4CYP1B1
ESTRADIOL4CYP1B1
CANNABIDIOL4CYP1B1
BERBERINE4CYP1B1
MELATONIN4CYP1B1
ERYTHROMYCIN4CYP1B1
CARVEDILOL4CYP1B1
RESVERATROL3CYP1B1
BERGAPTEN3CYP1B1
QUERCETIN3CYP1B1
CANNABINOL3CYP1B1
LUTEOLIN2CYP1B1
FORMONONETIN2CYP1B1
FLAVONE2CYP1B1
2-METHOXYESTRADIOL2CYP1B1
PINOCEMBRIN2CYP1B1
KHELLIN2CYP1B1
BAICALEIN2CYP1B1
PTEROSTILBENE2CYP1B1
KAEMPFEROL1CYP1B1
PLUMBAGIN1CYP1B1

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)1CYP1B1
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug2PXDN, CPAMD8
EDifficult family or no structure, no drug2LTBP2, LTBP3

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
PXDN0
CPAMD80
LTBP20
LTBP30

Clinical trials & evidence

Clinical trials

Clinical trials: 0.