Detecting the Difficult: An Intronic NPC1 Variant Hiding in Plain Sight

Area of Science:

• Genetics
• Molecular Biology
• Medical Diagnostics

Background:

• Niemann-Pick Type C (NPC) disease is an autosomal recessive disorder.
• Accurate genetic diagnosis requires identifying biallelic pathogenic variants.
• Next Generation Sequencing (NGS) is a primary tool for genetic variant detection.

Observation:

• A 14-year-old male with biochemically confirmed NPC disease initially showed only a heterozygous pathogenic variant.
• Manual review of NGS data revealed a rare intronic variant (c.709C>T; p.Pro237Ser) near homopolymers.
• This variant was initially overlooked due to its benign classification and potential NGS detection issues.

Findings:

• The identified intronic variant (c.709C>T) was associated with a second rare intronic NPC1 variant (c.1947+5G>C).
• The second variant (c.1947+5G>C) utilized a cryptic splice donor site, confirmed by Sanger sequencing.
• Together, these variants explain the patient's Niemann-Pick Type C disease diagnosis.

Implications:

• Manual data review is essential for detecting rare intronic variants missed by automated analysis.
• Short-read NGS technologies may struggle with variants near homopolymers, necessitating careful evaluation.
• Identifying all causative variants is critical for accurate diagnosis, treatment, and family genetic screening in inherited disorders.