Divergent epigenetic profile underlie pubertal disorders in MKRN3-associated central precocious puberty and...

MKRN3 gene loss-of-function mutations cause central precocious puberty (CPP), whereas its deletion in Prader-Willi syndrome (PWS) paradoxically leads to hypogonadism. The mechanistic basis for these opposing reproductive phenotypes remains largely unclear.

We performed whole-exome sequencing in 98 Chinese CPP patients along with a systematic review of previously reported MKRN3 pathogenic and likely pathogenic variants to summarize genotype-phenotype correlations. Subsequently, genome-wide DNA methylation profiling was performed in CPP patients with the MKRN3 pathogenic variant, and the results were compared with those of patients with PWS, idiopathic CPP, and healthy controls.

A pathogenic frameshift MKRN3 variant [c.476dupC (p.Ala159fs*15)], representing the first frameshift mutation reported within the inter-C3H1 hotspot region in an Asian cohort, was identified. Patients with severe MKRN3 variants exhibited significantly earlier pubertal onset (5.80 vs. 7.50 years, P = 0.029) and higher GnRH-stimulated peak LH levels (34.55 vs. 11.00 IU/L, P = 0.047) than those with missense mutations. Methylation analysis revealed no differences in MKRN3 but identified 18,609 differentially methylated positions between MKRN3-CPP and PWS. Key findings included hypermethylation of IGSF10 (Δβ = 0.37), ZC3H18 (Δβ = 0.27), SH3RF3 (Δβ = 0.36), and PTH1R (Δβ = 0.28), alongside hypomethylation of MAGEL2 (Δβ = - 0.19), and PTPA (Δβ = - 0.23), where Δβ represents the difference in DNA methylation β values between groups.

We identified a first frameshift pathogenic variant localized to the inter-C3H1 region in Asia, further confirming its functional significance. Our study suggests an epigenetic framework that could potentially explain how divergent pubertal phenotypes in MKRN3 deficiency might arise from dysregulated epigenetic programming of downstream neuroendocrine pathways.