Kallmann Syndrome: Functional Analysis of a CHD7 Missense Variant Shows Aberrant RNA Splicing

Area of Science:

• Genetics
• Endocrinology
• Neuroscience

Background:

• Kallmann syndrome is a rare genetic disorder causing hypogonadotropic hypogonadism and impaired smell due to GnRH and olfactory neuron defects.
• Genetic testing for Kallmann syndrome often identifies variants of uncertain significance (VUS) requiring functional validation.
• The CHD7 gene is implicated in Kallmann syndrome, but the functional impact of specific variants, like missense VUS, needs clarification.

Purpose of the Study:

• To functionally analyze a heterozygous missense VUS (c.4354G>T, p.Val1452Leu) in the CHD7 gene from a Kallmann syndrome patient.
• To determine the effect of this VUS on RNA splicing using minigene assays.
• To reclassify the VUS based on functional consequences and improve genetic diagnosis for Kallmann syndrome.

Main Methods:

• Minigene assays were employed to assess the splicing impact of the CHD7 c.4354G>T variant.
• Analysis of RNA transcripts generated by the variant to identify splicing abnormalities.
• Structural analysis of the CHD7 protein to understand the consequences of the observed splicing defect.

Main Results:

• The c.4354G>T variant in CHD7 led to aberrant RNA splicing, producing a transcript lacking exon 19.
• This abnormal splicing resulted in an in-frame deletion (p.Val1452_Lys1511del) within the helicase C-terminal domain of the CHD7 protein.
• The identified variant was reclassified from VUS to likely pathogenic based on these functional findings.

Conclusions:

• Missense variants can cause significant RNA splicing defects beyond simple amino acid changes.
• Functional analysis is crucial for reclassifying VUS and achieving accurate genetic diagnoses in disorders like Kallmann syndrome.
• This study highlights the importance of investigating splicing alterations in genetic variant interpretation.