Functional Characterization of a Novel Splice-Altering Intronic Variant in AMPD2 Associated with Pontocerebellar...

Area of Science:

• Genetics
• Neurology
• Molecular Biology

Background:

• A two-year-old female presented with speech and gait disturbances, strabismus, hypotonia, and spasticity.
• Previous genetic tests for spinal muscular atrophy, chromosomal microarray, and karyotype were normal.
• Facial dysmorphic features included low-set ears, strabismus, downslanting palpebral fissures, and micrognathia.

Purpose of the Study:

• To investigate the genetic cause of the patient's complex neurological phenotype.
• To characterize a novel homozygous variant in the AMPD2 gene.
• To confirm the functional impact of the identified variant on gene splicing.

Main Methods:

• Trio exome sequencing was performed on the patient and her parents.
• Analysis identified a homozygous variant (c.353+11C>T) in the AMPD2 gene.
• RNA extraction, cDNA analysis (gel electrophoresis, Sanger sequencing), and quantitative PCR were used to confirm alternative splicing.

Main Results:

• A homozygous splice-altering variant in the AMPD2 gene was identified.
• The patient's phenotype showed partial consistency with pontocerebellar hypoplasia type 9 (PCH9).
• Functional studies confirmed the variant creates a novel splicing site, leading to alternative splicing.

Conclusions:

• This study designates the early-onset phenotype of PCH9 associated with a splice-altering AMPD2 variant.
• Functional studies are crucial for evaluating intronic variants of uncertain significance.
• Validated variants provide critical insights for clinical decision-making and family reproductive planning.