Identification of a PATL2 missense variant (c.877G>T) disrupting canonical splicing and contributing to female infertility

TL;DR

A specific missense variant in the PATL2 gene disrupts splicing and contributes to female infertility, providing new insights into its role in reproductive health.

Contribution

First experimental evidence that the PATL2 c.877G>T missense variant causes pathogenic splicing, enabling its reclassification.

Findings

The PATL2 c.877G>T variant disrupts canonical splicing, leading to exon 12 skipping.

Biallelic PATL2 variants co-segregate with infertility in the studied family.

Functional assays confirm the pathogenicity of the c.877G>T variant.

Abstract

PATL2 deficiency is a significant cause of female infertility. Although multiple PATL2 missense variants have been reported in prior studies, a number of these variants remain classified as variants of uncertain significance (VUS).

We present a patient of primary infertility characterized by oocyte maturation disorders and fertilization failure. Comprehensive genetic analysis was conducted through whole-exome sequencing (WES) to identify pathogenic variants, followed by Sanger sequencing for familial co-segregation analysis. Reverse transcription (RT-PCR), cDNA sequencing and quantitative RT-PCR were performed to validate the effect of the variant on pre-mRNA splicing.

We identified compound heterozygous variants in the PATL2 gene by WES: a pathogenic splice-site splicing variant (c.223-14_223-2del) and a missense variant (c.877G>T) initially classified as a VUS. Sanger sequencing confirmed that the proband carried biallelic variants, whereas her sisters with either wild-type genotypes or a single heterozygous variant exhibited normal fertility, supporting the co-segregation of the identified variants. Critically, RNA assays demonstrated that the missense variant c.877G>T disrupts canonical splicing of PATL2, resulting in exon 12 skipping.

This study provides the first experimental evidence that a PATL2 missense variant (c.877G>T) can exert its pathogenicity through aberrant splicing, supporting its pathogenic reclassification and elucidating a genotype-phenotype correlation for PATL2 missense variants through functional assays.

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