Variegate porphyria

disease
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Also known as porphyria variegateProtocoproporphyriaprotoporphyrinogen oxidase deficiencyVP

Summary

Variegate porphyria (MONDO:0008297) is a disease caused by PPOX (GenCC Definitive), with 5 cohort genes and 6 clinical trials. Top therapeutic interventions include afamelanotide, hemin, and givosiran.

At a glance

  • Prevalence: 1-9 / 1 000 000 (France) [Orphanet-validated]
  • Causal gene: PPOX (GenCC Definitive)
  • Cohort genes: 5
  • ClinVar variants: 77
  • Phenotypes (HPO): 48
  • Clinical trials: 6

Clinical features

Epidemiology

Prevalence records

22 prevalence record(s), Orphanet, top 20 (validated / broadest geography first):

TypeClassValueGeographyValidation
Annual incidence<1 / 1 000 0000.012FranceValidated
Annual incidence<1 / 1 000 0000.006FinlandValidated
Annual incidence<1 / 1 000 0000.016IrelandValidated
Annual incidence<1 / 1 000 0000.006ItalyValidated
Annual incidence<1 / 1 000 0000.006NetherlandsValidated
Annual incidence<1 / 1 000 0000.007NorwayValidated
Annual incidence<1 / 1 000 0000.004SpainValidated
Annual incidence<1 / 1 000 0000.011SwedenValidated
Annual incidence<1 / 1 000 0000.026SwitzerlandValidated
Annual incidence<1 / 1 000 0000.008United KingdomValidated
Point prevalence1-9 / 1 000 0000.48FranceValidated
Point prevalence1-9 / 1 000 0000.24FinlandValidated
Point prevalence1-9 / 1 000 0000.64IrelandValidated
Point prevalence1-9 / 1 000 0000.24NetherlandsValidated
Point prevalence1-9 / 1 000 0000.24ItalyValidated
Point prevalence1-9 / 1 000 0000.28NorwayValidated
Point prevalence1-9 / 1 000 0000.16SpainValidated
Point prevalence1-9 / 1 000 0000.44SwedenValidated
Point prevalence1-9 / 100 0001.04SwitzerlandValidated
Point prevalence1-9 / 1 000 0000.32United KingdomValidated

Signs & symptoms

Clinical features (HPO)

48 HPO clinical features (Orphanet curated; top 48 by frequency):

HPO IDTermFrequency
HP:0002027Abdominal painVery frequent (80-99%)
HP:0010472Abnormal circulating porphyrin concentrationVery frequent (80-99%)
HP:0010473PorphyrinuriaVery frequent (80-99%)
HP:0012217Increased urinary porphobilinogenVery frequent (80-99%)
HP:0012379Abnormal enzyme/coenzyme activityVery frequent (80-99%)
HP:0000707Abnormality of the nervous systemFrequent (30-79%)
HP:0000708Atypical behaviorFrequent (30-79%)
HP:0000739AnxietyFrequent (30-79%)
HP:0000992Cutaneous photosensitivityFrequent (30-79%)
HP:0001324Muscle weaknessFrequent (30-79%)
HP:0002019ConstipationFrequent (30-79%)
HP:0002273TetraparesisFrequent (30-79%)
HP:0003163Elevated urinary delta-aminolevulinic acidFrequent (30-79%)
HP:0003418Back painFrequent (30-79%)
HP:0007178Motor polyneuropathyFrequent (30-79%)
HP:0008066Abnormal blistering of the skinFrequent (30-79%)
HP:0008997Proximal muscle weakness in upper limbsFrequent (30-79%)
HP:0100749Chest painFrequent (30-79%)
HP:0200037Skin vesicleFrequent (30-79%)
HP:0200041Skin erosionFrequent (30-79%)
HP:0000011Neurogenic bladderOccasional (5-29%)
HP:0000822HypertensionOccasional (5-29%)
HP:0000953Hyperpigmentation of the skinOccasional (5-29%)
HP:0000998HypertrichosisOccasional (5-29%)
HP:0001010Hypopigmentation of the skinOccasional (5-29%)
HP:0001056MiliaOccasional (5-29%)
HP:0001072Thickened skinOccasional (5-29%)
HP:0001250SeizureOccasional (5-29%)
HP:0001265HyporeflexiaOccasional (5-29%)
HP:0001347HyperreflexiaOccasional (5-29%)
HP:0001649TachycardiaOccasional (5-29%)
HP:0002018NauseaOccasional (5-29%)
HP:0002203Respiratory paralysisOccasional (5-29%)
HP:0002595IleusOccasional (5-29%)
HP:0002902HyponatremiaOccasional (5-29%)
HP:0002910Elevated circulating hepatic transaminase concentrationOccasional (5-29%)
HP:0003474Somatic sensory dysfunctionOccasional (5-29%)
HP:0011355Localized skin lesionOccasional (5-29%)
HP:0012332Abnormal autonomic nervous system physiologyOccasional (5-29%)
HP:0031218Inappropriate antidiuretic hormone secretionOccasional (5-29%)
HP:0100699ScarringOccasional (5-29%)
HP:0000738HallucinationsVery rare (<1-4%)
HP:0001259ComaVery rare (<1-4%)
HP:0001392Abnormality of the liverVery rare (<1-4%)
HP:0001402Hepatocellular carcinomaVery rare (<1-4%)
HP:0001903AnemiaVery rare (<1-4%)
HP:0011999ParanoiaVery rare (<1-4%)
HP:0012622Chronic kidney diseaseVery rare (<1-4%)

Identifiers

Disease identifiers

FieldValue
Canonical namevariegate porphyria
Mondo IDMONDO:0008297
MeSHD046350
OMIM176200
Orphanet79473
DOIDDOID:4346
ICD-111227474618
NCITC85219
SNOMED CT58275005
UMLSC0162532
MedGen58118
GARD0007848
NORD1821
Is cancer (heuristic)no

Also known as: porphyria variegate · Protocoproporphyria · protoporphyrinogen oxidase deficiency · variegate porphyria · VP

Data availability: 77 ClinVar variants · 6 GenCC gene-disease records · 1 cell line.

Disease family

An umbrella term covering 1 Mondo subtype.

Classification path: disease › human disease › disease by body system or component › digestive system disorderhepatobiliary disorderliver disorderhepatic porphyria › PPOX-related hepatic porphyria › variegate porphyria

Subtypes (1): variegate porphyria, childhood-onset

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

77 retrieved; paginated sample, class counts are floors:

28 uncertain significance, 15 conflicting classifications of pathogenicity, 11 pathogenic, 7 likely pathogenic, 5 pathogenic/likely pathogenic, 5 benign/likely benign, 3 benign, 1 conflicting classifications of pathogenicity; other, 1 likely benign, 1 conflicting classifications of pathogenicity; other; risk factor

ClinVarVariant (HGVS)GeneClassificationReview
559476Single allelePathogeniccriteria provided, single submitter
2500825NM_001122764.3(PPOX):c.420del (p.Glu141fs)B4GALT3Pathogeniccriteria provided, single submitter
1065637NM_000410.4(HFE):c.1006+1G>AHFEPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
407079NM_000410.4(HFE):c.546_547del (p.Leu183fs)HFEPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1704297NM_001122764.3(PPOX):c.338G>C (p.Arg113Thr)PPOXPathogenicno assertion criteria provided
189241NM_001122764.3(PPOX):c.199del (p.Ala66_Leu67insTer)PPOXPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
664759NM_001122764.3(PPOX):c.745dup (p.Val249fs)PPOXPathogeniccriteria provided, multiple submitters, no conflicts
8693NM_001122764.3(PPOX):c.694G>C (p.Gly232Arg)PPOXPathogeniccriteria provided, single submitter
8694NM_001122764.3(PPOX):c.502C>T (p.Arg168Cys)PPOXPathogenic/Likely pathogenicno assertion criteria provided
8695NM_001122764.3(PPOX):c.59A>C (p.His20Pro)PPOXPathogenicno assertion criteria provided
8696NM_001122764.3(PPOX):c.175C>T (p.Arg59Trp)PPOXPathogeniccriteria provided, multiple submitters, no conflicts
8697NM_001122764.3(PPOX):c.503G>A (p.Arg168His)PPOXPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
8699NM_001122764.3(PPOX):c.538_539del (p.Ile180fs)PPOXPathogenicno assertion criteria provided
8700NM_001122764.3(PPOX):c.1241_1245del (p.Leu414fs)PPOXPathogenicno assertion criteria provided
8702PPOX, IVS11DS, G-A, -1PPOXPathogenicno assertion criteria provided
8703NM_001122764.3(PPOX):c.35T>C (p.Ile12Thr)PPOXPathogenicno assertion criteria provided
3067865NM_001122764.3(PPOX):c.87+1G>APPOXLikely pathogeniccriteria provided, single submitter
3362804NM_001122764.3(PPOX):c.313dup (p.Leu105fs)PPOXLikely pathogeniccriteria provided, single submitter
3775017NM_001122764.3(PPOX):c.1123C>T (p.Gln375Ter)PPOXLikely pathogeniccriteria provided, single submitter
4535974NM_001122764.3(PPOX):c.917T>C (p.Leu306Pro)PPOXLikely pathogeniccriteria provided, single submitter
4846908NM_001122764.3(PPOX):c.362_363del (p.Pro121fs)PPOXLikely pathogeniccriteria provided, single submitter
623210NM_001122764.3(PPOX):c.869-3_869-2delPPOXLikely pathogeniccriteria provided, single submitter
976468NM_001122764.3(PPOX):c.1291+1G>TPPOXLikely pathogenicno assertion criteria provided
1284646NM_005689.4(ABCB6):c.1762G>A (p.Gly588Ser)ABCB6Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
68473NM_005689.4(ABCB6):c.575G>A (p.Arg192Gln)ABCB6Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
10NM_000410.4(HFE):c.187C>G (p.His63Asp)HFEConflicting classifications of pathogenicity; othercriteria provided, conflicting classifications
11NM_000410.4(HFE):c.193A>T (p.Ser65Cys)HFEConflicting classifications of pathogenicitycriteria provided, conflicting classifications
9NM_000410.4(HFE):c.845G>A (p.Cys282Tyr)HFEConflicting classifications of pathogenicity; other; risk factorcriteria provided, conflicting classifications
1668855NM_001122764.3(PPOX):c.1296A>G (p.Ser432=)PPOXConflicting classifications of pathogenicitycriteria provided, conflicting classifications
293239NM_001122764.3(PPOX):c.-246G>TPPOXConflicting classifications of pathogenicitycriteria provided, conflicting classifications

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 7 · Orphanet: 15 · 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
PPOXDefinitiveSemidominantvariegate porphyria7

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
PPOXOrphanet:79473Variegate porphyria
ABCB6Orphanet:241Dyschromatosis universalis hereditaria
ABCB6Orphanet:90044Familial pseudohyperkalemia
ABCB6Orphanet:98938Colobomatous microphthalmia
ABCB6Orphanet:98942Coloboma of choroid and retina
ABCB6Orphanet:98943Coloboma of eye lens
ABCB6Orphanet:98944Coloboma of iris
ABCB6Orphanet:98945Coloboma of macula
ABCB6Orphanet:98946Coloboma of eyelid
ABCB6Orphanet:98947Coloboma of optic disc
HFEOrphanet:443057Sporadic porphyria cutanea tarda
HFEOrphanet:443062Familial porphyria cutanea tarda
HFEOrphanet:465508Symptomatic form of HFE-related hemochromatosis
HFEOrphanet:586Cystic fibrosis
HFEOrphanet:648581Digenic hemochromatosis

Cohort genes → proteins

5 cohort genes, 4 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence5

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
PPOXHGNC:9280ENSG00000143224P50336Protoporphyrinogen oxidasegencc,clinvar
ABCB6HGNC:47ENSG00000115657Q9NP58ATP-binding cassette sub-family B member 6clinvar
HFEHGNC:4886ENSG00000010704Q30201Hereditary hemochromatosis proteinclinvar
HFE-AS1HGNC:55168HFE antisense RNA 1clinvar
B4GALT3HGNC:926ENSG00000158850O60512Beta-1,4-galactosyltransferase 3clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
PPOXProtoporphyrinogen oxidaseCatalyzes the 6-electron oxidation of protoporphyrinogen-IX to form protoporphyrin-IX.
ABCB6ATP-binding cassette sub-family B member 6ATP-dependent transporter that catalyzes the transport of a broad-spectrum of porphyrins from the cytoplasm to the extracellular space through the plasma membrane or into the vesicle lumen.
HFEHereditary hemochromatosis proteinBinds to transferrin receptor (TFR) and reduces its affinity for iron-loaded transferrin.
B4GALT3Beta-1,4-galactosyltransferase 3Responsible for the synthesis of complex-type N-linked oligosaccharides in many glycoproteins as well as the carbohydrate moieties of glycolipids.

Protein-family classification

Druggable: 3 · Difficult: 0 · Unknown: 2 · Druggable fraction: 0.6

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
Transporter115.6×0.251
Antibody/Immunoglobulin15.8×0.320
Enzyme (other)12.4×0.471
Other/Unknown20.7×0.877

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
PPOXEnzyme (other)yes1.3.3.4Amino_oxidase, Protoporphyrinogen_oxidase, FAD/NAD-bd_sf
ABCB6TransporteryesABC_transporter-like_ATP-bd, AAA+_ATPase, ABC1_TM_dom
HFEAntibody/ImmunoglobulinyesMHC_I_a_a1/a2, Ig/MHC_CS, Ig_C1-set
HFE-AS1Other/Unknownno
B4GALT3Other/UnknownnoGalactosyl_T, Galactosyl_T_C, Galactosyl_T_N

Expression context

Cohort genes with no expression data: 1.

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)4
unknown1

Top tissues across cohort

TissueCohort genes
epithelium of bronchus1
olfactory segment of nasal mucosa1
right uterine tube1
left ovary1
right hemisphere of cerebellum1
right ovary1
olfactory bulb1
stromal cell of endometrium1
type B pancreatic cell1
granulocyte1
oocyte1
secondary oocyte1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
PPOX264ubiquitousmarkerright uterine tube, olfactory segment of nasal mucosa, epithelium of bronchus
ABCB6140ubiquitousmarkerright ovary, right hemisphere of cerebellum, left ovary
HFE238ubiquitousmarkertype B pancreatic cell, olfactory bulb, stromal cell of endometrium
HFE-AS1
B4GALT3284ubiquitousmarkeroocyte, granulocyte, secondary oocyte

Protein interactions among cohort

Intra-cohort edges: 1.

Hub genes (top 10 by interactor count)

SymbolInteractor count
HFE1,569
PPOX1,525
ABCB61,480
B4GALT31,085
HFE-AS10

Intra-cohort edges

ABSources
ABCB6PPOXstring_interaction

Structural data

PDB: 3 · AlphaFold-only: 1 · No structure: 1

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
ABCB6Q9NP5816
PPOXP503363
HFEQ302012

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
B4GALT3O6051288.72

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 20. 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
Defective ABCB6 causes MCOPCB712855.0×0.007ABCB6
Mitochondrial ABC transporters1713.8×0.014ABCB6
Heme biosynthesis1190.3×0.024PPOX
N-Glycan antennae elongation1190.3×0.024B4GALT3
N-glycan antennae elongation in the medial/trans-Golgi1142.8×0.024B4GALT3
Keratan sulfate/keratin metabolism1124.1×0.024B4GALT3
ABC transporter disorders1109.8×0.024ABCB6
Keratan sulfate biosynthesis195.2×0.024B4GALT3
Transferrin endocytosis and recycling192.1×0.024HFE
Glycosaminoglycan metabolism154.9×0.036B4GALT3
Disorders of transmembrane transporters134.8×0.051ABCB6
ABC-family protein mediated transport130.4×0.051ABCB6
Metabolism of carbohydrates and carbohydrate derivatives130.1×0.051B4GALT3
Transport to the Golgi and subsequent modification125.7×0.055B4GALT3
Asparagine N-linked glycosylation115.0×0.087B4GALT3
Transport of small molecules16.3×0.187ABCB6
Post-translational protein modification14.8×0.227B4GALT3
Disease13.3×0.301ABCB6
Metabolism of proteins13.1×0.301B4GALT3
Metabolism12.9×0.302B4GALT3

GO biological processes 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.

GO termCohort genesFoldFDRSample cohort genes
porphyrin-containing compound biosynthetic process22106.5×1e-05PPOX, ABCB6
intracellular iron ion homeostasis2122.1×0.002ABCB6, HFE
tetrapyrrole metabolic process14213.0×0.003ABCB6
negative regulation of antigen processing and presentation of endogenous peptide antigen via MHC class I14213.0×0.003HFE
regulation of iron ion transport12106.5×0.003HFE
heme transmembrane transport12106.5×0.003ABCB6
glucosylceramide metabolic process11404.3×0.003B4GALT3
cellular detoxification of cadmium ion11404.3×0.003ABCB6
response to iron ion starvation11404.3×0.003HFE
porphyrin-containing compound metabolic process11053.2×0.003ABCB6
heme transport11053.2×0.003ABCB6
negative regulation of CD8-positive, alpha-beta T cell activation11053.2×0.003HFE
galactosylceramide biosynthetic process1842.6×0.004B4GALT3
heme metabolic process1842.6×0.004ABCB6
negative regulation of T cell cytokine production1601.9×0.005HFE
cellular response to iron ion1601.9×0.005HFE
obsolete protoporphyrinogen IX biosynthetic process1421.3×0.005PPOX
heme B biosynthetic process1421.3×0.005PPOX
regulation of protein localization to cell surface1421.3×0.005HFE
heme A biosynthetic process1383.0×0.005PPOX
transferrin transport1383.0×0.005HFE
urate metabolic process1383.0×0.005HFE
positive regulation of peptide hormone secretion1383.0×0.005HFE
hormone biosynthetic process1351.1×0.005HFE
intracellular copper ion homeostasis1234.1×0.007ABCB6
response to iron ion1234.1×0.007HFE
melanosome assembly1221.7×0.007ABCB6
negative regulation of ubiquitin-dependent protein catabolic process1210.7×0.007HFE
positive regulation of receptor-mediated endocytosis1200.6×0.008HFE
heme biosynthetic process1150.5×0.010PPOX

Therapeutics

Drugs indicated for this disease

No approved or late-stage (phase ≥3) drug is indicated for this disease; the following are in earlier-phase trials only.

Earlier-phase candidates (phase 2, investigational — efficacy not yet established): Afamelanotide, Hemin.

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 5

Druggability breadth: 2 of 5 evidence-associated genes (40%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

SymbolMoleculesMax phase
PPOX00
ABCB600
HFE00
HFE-AS100
B4GALT300

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

SymbolAssaysType breakdown
PPOX5Binding:5
ABCB63Functional:3

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
PPOX1.3.3.4protoporphyrinogen oxidase

Pharmacogenomics

Cohort genes with a PharmGKB record: 4; 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 drug3PPOX, ABCB6, HFE
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug2HFE-AS1, B4GALT3

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
PPOX5
ABCB63
HFE0
HFE-AS10
B4GALT30

Clinical trials & evidence

Clinical trials

Clinical trials: 6.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified3
PHASE22
PHASE31

Top trials by phase / activity

NCTPhaseStatusTitle
NCT03338816PHASE3COMPLETEDENVISION: A Study to Evaluate the Efficacy and Safety of Givosiran (ALN-AS1) in Patients With Acute Hepatic Porphyrias (AHP)
NCT02922413PHASE2TERMINATEDPanhematin for Prevention of Acute Attacks of Porphyria
NCT05854784PHASE2COMPLETEDStudy to Evaluate the Safety and Efficacy of Afamelanotide in Patients With Variegate Porphyria (VP)
NCT02935400Not specifiedACTIVE_NOT_RECRUITINGAcute Porphyria Biomarkers for Disease Activity
NCT01568554Not specifiedCOMPLETEDClinical Diagnosis of Acute Porphyria
NCT03547297Not specifiedTERMINATEDINSIGHT-AHP: A Study to Characterize the Prevalence of Acute Hepatic Porphyria (AHP) in Patients With Clinical Presentation and History Consistent With AHP

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
AFAMELANOTIDE41
HEMIN32
GIVOSIRAN31
CHEMBL430366402
CHEMBL530847902
HEMATIN-12