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Background  Salivary amylase in humans is encoded by the copy variable gene  AMY1  in the amylase gene cluster on chromosome 1. Although the role of salivary amylase is well established, the consequences of the copy number variation (CNV) at  AMY1  on salivary amylase protein production are less well understood. The amylase gene cluster is highly structured with a fundamental difference between odd and even  AMY1  copy number haplotypes. In this study, we aimed to explore, in samples from 119 unrelated individuals, not only the effects of  AMY1  CNV on salivary amylase protein expression and amylase enzyme activity but also whether there is any evidence for underlying difference between the common haplotypes containing odd numbers of  AMY1  and even copy number haplotypes.    Results    AMY1  copy number was significantly correlated with the variation observed in salivary amylase production (11.7% of variance,  P  < 0.0005) and enzyme activity (13.6% of variance,  P  < 0.0005) but did not explain the majority of observed variation between individuals.  AMY1 -odd and  AMY1 -even haplotypes showed a different relationship between copy number and expression levels, but the difference was not statistically significant ( P  = 0.052).    Conclusions  Production of salivary amylase is correlated with  AMY1  CNV, but the majority of interindividual variation comes from other sources. Long-range haplotype structure may affect expression, but this was not significant in our data.    Electronic supplementary material  The online version of this article (doi:10.1186/s40246-017-0097-3) contains supplementary material, which is available to authorized users.

Copy number variation of human AMY1 is a minor contributor to variation in salivary amylase expression and activity