Reclassification of the HPGD p.Ala13Glu variant causing primary hypertrophic osteoarthropathy

Here, we highlight the case of a 31-yr-old man who had clinical features of primary hypertrophic osteoarthropathy (PHOAR) and harbored a homozygous variant (c.38C > A, p.Ala13Glu) in the HPGD gene, as indicated by whole-exome sequencing (WES). This variant has been previously classified by our laboratory as a variant of uncertain significance (VUS). However, another patient with the same phenotype and the same homozygous variant in HPGD was subsequently reported. In reassessing the variant, the absence of this variant in the gnomAD population database, supporting computational predictions, observation in homozygosity in two probands, and specificity of the phenotype for HPGD, all provide sufficient evidence to reclassify the HPGD c.38C > A, p.Ala13Glu variant as likely pathogenic.

To determine the inheritance, both mother and father, who were asymptomatic, were screened for the variant, and they were found to be heterozygous, confirming autosomal recessive inheritance.The variant is absent in the gnomAD population database (PM2_Supporting).
Another individual with the same phenotype (severe polyarthralgia, enlargement of the fingertips and toes, coarse facial features, prominent facial folds in the forehead, digital clubbing) who harbors the same homozygous variant in HPGD was subsequently reported (González et al. 2022), allowing application of PM3 given the now two homozygous individuals, per ClinGen guidance (https://clinicalgenome.org/site/assets/files/3717/svi_proposal_ for_pm3_criterion_-_version_1.pdf).Additionally, PP4_Moderate was applied given that the phenotype is highly specific for the HPGD gene.
The HPGD gene is located on Chromosome 4 (Table 1) and encodes a 266-amino acid protein.This gene encodes a member of the short-chain nonmetalloenzyme alcohol dehydrogenase protein family.The encoded enzyme catalyzes the NAD-dependent oxidation of a broad range of hydroxylated polyunsaturated fatty acids (eicosanoids, docosanoids, including prostaglandins, lipoxins, and resolvins), producing their corresponding keto (oxo) metabolites.The enzyme reduces the levels of proproliferative prostaglandins, such as prostaglandin E2, and generates oxo-fatty acid products that can profoundly influence cell function by abolishing proinflammatory cytokine expression.It converts resolvins E1, D1, and D2 to their oxo products, which represents a mode of resolvin inactivation.Resolvin E1 plays an important role during the resolution phase of acute inflammation, whereas resolvins D1 and D2 have a unique role in obesity-induced adipose inflammation (Surhone et al. 2011;Stelzer et al. 2016).Pathogenic variants are located throughout the gene.In this case, the variant is located in the first turn of the protein and changes alanine to glutamic acid before the start of the protein helix.This change could alter the proper conformation around the substrate binding site, blocking or inhibiting the adequate union of the enzyme to the substrate.The clinical and physiological manifestations of PHOAR are related to the activity of prostaglandin E (Uppal et al. 2008;Sasaki et al. 2012).Not all patients, including the one presented here, manifest PHOAR from birth.In this case, our patient showed overgrowth of both hands  Reclassification of the HPGD p.Ala13Glu variant Molecular Case Studies and feet since puberty, and this was associated with joint pain.Additionally, prostaglandin E2 exhibits strong peripheral vasodilatory activity, which may explain finger clubbing and skin thickening due to prolonged local vasodilation (Uppal et al. 2008).The patient presented with skin thickening, palmoplantar hyperkeratosis, and hyperhidrosis.The clinical signs and symptoms of the disease tend to stabilize over time, and there is no specific treatment.However, there are therapeutic options for the control of symptoms with aspirin, nonsteroidal anti-inflammatory drugs (NSAIDs), systemic corticosteroids, and colchicine.Plastic surgery is reserved for patients with significant eyelid ptosis or severe aesthetic problems (Salah et al. 2019).In this case, controlling the patient's joint pain was difficult using aspirin and NSAIDs.Currently, he has no intention of undergoing plastic surgery.Inheritance patterns in PHOAR vary according to the study.Initially, PHOAR genes were first found in consanguineous families, suggesting autosomal recessive inheritance.Nonetheless, other studies have supported autosomal dominant transmission with incomplete penetrance (Castori et al. 2005).Similarly, its expression varies by sex, with a higher tendency in males, and presents an early puberty onset.However, in this patient, the symptoms manifested during early adulthood.PHOAR 2 tends to have a more skewed sex ratio than PHOAR 1.Some studies have demonstrated that prostaglandin transport is influenced by sex hormones.
Regarding the current patient, gastrointestinal alterations have been reported in PHOAR.Castori et al. (2005) noted that gastrointestinal involvement varies depending on the inheritance pattern of the condition, including chronic gastritis, hypertrophic gastropathy, peptic ulcer, and Crohn's disease.The overall prevalence of gastrointestinal signs was 10%-12%.Although Crohn's disease and peptic ulcers were observed in both dominant and recessive forms, chronic/hypertrophic gastritis is more common in the autosomal dominant form.
In Colombia, only two cases of PHO have been published.One case was a clinical diagnosis in a 17-yr-old patient (Moreno et al. 2010), and the other case, as described above, was a molecular diagnosis with the variant classified as a VUS (González et al. 2022).Furthermore, our patient presented clinical features of PHO and carried the same variant that was previously reported in ClinVar as a VUS.The absence of this variant in the gnomAD population database, computational predictions, observation in homozygosity in two probands, and specificity of the phenotype for HPGD provide sufficient evidence to reclassify the HPGD c.38C > A, p.Ala13Glu variant as likely pathogenic.
In conclusion, we describe the reclassification of a variant in the HPGD gene that is associated with primary hypertrophic osteoarthropathy.To our knowledge, this is the second Colombian patient with molecular confirmation.Clinical evidence of overgrowth, arthralgia, skin thickening, and gastrointestinal manifestations should raise suspicion of PHOAR and prompt genetic testing.Further research is required to explore prognosis, new therapeutic interventions, and functional studies of the variant to demonstrate pathogenicity in vitro.
Reclassification of the HPGD p.Ala13Glu variantC O L D S P R I N G H A R B O RMolecular Case Studies

Table 1 .
Variant interpretation of HPGD