Alternative transcripts in variant interpretation: the potential for missed diagnoses and misdiagnoses

Area of Science:

• Genomic medicine
• Molecular diagnostics

Background:

• Professional guidelines recommend using biologically relevant transcripts for variant pathogenicity assessment.
• Laboratory practices in transcript selection show variability, potentially impacting diagnostic accuracy.

Purpose of the Study:

• To illustrate the impact of alternative transcript and tissue expression considerations on genomic testing accuracy.
• To highlight potential pitfalls in variant pathogenicity assessment due to non-consideration of alternative transcripts.

Main Methods:

• Case series describing three patients with incorrect genomic results.
• Analysis of genomic data, focusing on transcript selection and tissue expression patterns.

Main Results:

• A pathogenic variant in a brain-expressed isoform of CKDL5 was missed due to intronic location in analyzed transcripts.
• A microdeletion in KMT2C affecting a brain-expressed isoform was initially unreported, leading to a Kleefstra syndrome diagnosis.
• A reported pathogenic variant in OFD1 was re-evaluated and determined not to be causative due to its absence in biologically relevant transcripts.

Conclusions:

• Failure to consider alternative transcripts can lead to incorrect genetic diagnoses.
• Alternative transcripts and tissue expression patterns are critical confounders in interpreting genetic test results, especially when discordant with clinical phenotype.