Gene Structure and Function
Core concepts
Know the anatomy of a eukaryotic gene: promoter and core elements, 5' UTR, exons and introns with canonical splice sites (GT-AG rule), branch point, 3' splice site, and 3' UTR with polyadenylation signal. Understand alternative splicing, alternative promoters, and tissue-specific expression, plus noncoding RNAs and their regulatory roles.
Be able to explain how mutations in different regions produce different effects: promoter variants affect expression level, splice-site variants cause exon skipping or intron retention, frameshifts alter downstream sequence, and 3' UTR variants may affect stability or microRNA binding. Know the concept of loss-of-function versus gain-of-function and haploinsufficiency.
Traps
Questions often test the GT-AG splice donor/acceptor rule and the consequence of a variant at the +1 or +2 position of an intron (classic splice donor, usually pathogenic). Another trap is assuming all exonic variants are coding; the 5' and 3' UTRs are exonic but noncoding. Distinguish a variant that creates a premature stop codon (nonsense-mediated decay may reduce transcript) from one that removes the normal stop codon.
Rule of thumb
Localize the variant first (promoter, 5' UTR, exon, intron, 3' UTR), then predict the mechanism. Splice-site positions +1/+2 (donor) and -1/-2 (acceptor) are the highest-yield pathogenic hotspots.
Worked example
A variant at c.1234+1G>T disrupts the canonical donor splice site, typically causing exon skipping or intron retention and loss of function, and should be interpreted as likely pathogenic even though it is intronic.