Molecular Genetics and Genomics
Core concepts
Know the central dogma in operational terms: transcription, splicing, translation, and how each step can be disrupted. Be fluent in variant nomenclature (HGVS: c. for coding DNA, p. for protein, g. for genomic) and variant classes - missense, nonsense, frameshift, splice-site, in-frame indel, synonymous, and regulatory/deep intronic. Understand loss-of-function vs gain-of-function mechanisms, haploinsufficiency, dominant-negative effects, and trinucleotide repeat instability.
Genomics concepts to master: gene structure (exons/introns, UTRs), population frequency databases (gnomAD), in silico predictors (CADD, REVEL, SpliceAI), ACMG/AMP variant classification (PVS1, PS, PM, PP, BA1, BS, BP criteria), and the difference between pathogenic, likely pathogenic, VUS, likely benign, benign. Understand penetrance, expressivity, and genotype–phenotype correlation.
Traps
A frequent trap is misclassifying a variant based only on in silico prediction - predictors support, they do not prove. Another is confusing a variant of uncertain significance with a benign variant; a VUS must not be used clinically to make decisions. Watch for splice-site variants reported as intronic but functionally significant, and for population frequency misinterpretation (a variant at 2% frequency is unlikely pathogenic for a rare dominant disorder unless it is a common low-penetrance allele).
Rule of thumb
PVS1 (null variant) applies only when loss-of-function is a known disease mechanism for that gene. Always check the gene–disease mechanism before invoking PVS1.
Worked example
A nonsense variant in a gene where disease arises by haploinsufficiency: PVS1 is applicable. The same nonsense variant in a gene where disease requires gain-of-function: PVS1 does not apply, and the variant may be a VUS.