Submission Details

The gene PPOX has been strongly associated with the disease variegate porphyria according to the gene-disease association criteria of the ACMG (SOP version 10). Previously, variegate porphyria was reported as two disease entities with differing modes of inheritance (autosomal recessive and autosomal dominant) (OMIM). Other papers have discussed the disease as autosomal dominant with incomplete penetrance (PMID: 29516370; 10870850). However, based on ACMG lumping and splitting criteria, variegate porphyria has been reclassified as semidominant due to its consistent molecular mechanism of disease and due to the observation that missense mutations that preserve 10–25% of PPOX activity may not cause clinically overt disease (PMID: 9811936).

Homozygous or biallelic pathogenic mutations, which severely reduce enzyme activity (<25% of normal), typically result in symptoms beginning before puberty. The reported symptoms include abnormal blistering of the skin, photosensitivity, brachydactyly, short stature, nystagmus, myopia, sensory neuropathy, intellectual disability, respiratory paralysis, and abnormal circulating porphyrin concentration in plasma, urine, and stool. Individuals who are heterozygous for pathogenic mutations are at risk for an acute attack, usually presenting with abdominal pain, post puberty onset of photosensitivity, or both. The accumulation of neurotoxic porphyrin precursors such as 5-aminolevulinic acid (ALA) and porphobilinogen (PBG), which are linear non-fluorescent molecules, is observed during acute attacks (PMID: 29516370). The accumulation of protoporphyrins, which are circular molecules that emit fluorescence when excited, is responsible for causing cutaneous photosensitivity. Although this disease has been categorized as one of the acute porphyrias, not all affected individuals experience acute attacks. Instead, symptoms are consistent with a spectrum of disease that worsens with lower enzyme activity and for which porphyrogenic agents (e.g. certain drugs, alcohol, low-carb diets, etc.) can induce an attack.

The gene PPOX encodes the enzyme protoporphyrinogen oxidase, which converts protoporphyrinogen-IX to protoporphyrin-IX. This enzyme is localized to the mitochondria and requires the cofactor FAD (vitamin B2). The protein primarily exists in vitro as a monomer but is expected to dimerize in vivo. Observed variegate porphyria mutations have been mapped to the PPOX structure and separated into the following different categories: affecting FAD binding (R59W, G11D, G11S, L15F, H20P, E34V, G40E, G40A, G232R, G232S, D349A, S350P, G448R, S450P, G453V, G453R), affecting substrate binding (R168H, R168C, G169E, A172V, G330R, G332A, V335G, Y348C, L401F), affecting the hydrophobic core (I12T, V84G, W224G and W224R, L236S, V282D, I283N, and A397D), affecting protein surface interactions (R38P, H106P, R138P, D143V, R152C, and R217C), and affecting protein secondary structure (L295, L444) (PMID: 21048046).

Summary of Case Level Data (10.8 points): 12 probands were scored with 14 unique variants (three nonsense and eleven missense variants).

Summary of Experimental Evidence (2 points): Biochemical characterization of the enzymatic reaction where purified WT and mutant protoporphyrinogen oxidase activity was assayed by measuring the velocity of the formation of protoporphyrin from protoporphyrinogen was scored. The high resolution crystal structure was also scored.

In summary, PPOX has been strongly associated with the semidominant condition, variegate porphyria.