You decide to carry out genetic association studies and identify a SNP variant that is found significantly more often in individuals who have schizophrenia than in those who are not affected. This SNP is found within an intron of the SZP gene
A. Can you deduce that an abnormality of the SZP gene is a cause of increased risk of schizophrenia?
B. Can you say whether the SNP variant itself is a cause?
A. No, you cannot be sure of this. The SZP gene would be a prime suspect, but the abnormality causing the heightened risk of schizophrenia might well lie instead in some other nearby gene.
B. No, you cannot say for certain. Most point mutations in introns have no functional effect, but some can be functionally important. For example, the intronic SNP might alter an enhancer element that is lying within the intron and is involved in the regulation of SZP transcription; or it might affect the splicing of the SZP gene transcripts.
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