In general, when you have a capital letter followed by a number and another capital letter, its usually the site of mutation. So, in proteomics, Y402H and A69S stands for the mutation from of Y(tyrosine)402 to H(histidine) and A(alanine) 69 to S(serine).

However, in most of the genetic studies related with association studies, they use the microsatellite markers( its the portion of gene which is conserved among the species and used for DNA mapping) on a specific chromosome to calculate LOD score which specifies whether there is a link of particular portion of gene with the diseased phenotype. Having said that, Y402H and A69S could very  well be among couple of microsatellite markers they used in this study.

About coding varient of gene, its just the splice variant. I suppose you are familiar with gene trascription, translation process. After gene trasncription, the m-RNA processing occurs, which actually leads to various splice varinats and is the reason of various isoforms of same protien and also non-functional or hyperfunctional protiens, causing loss-of-function, or gain-of-function features.

I hope this helps, or am I making your situation more complex. Honestly, I hate genetics paper, and I don't think I would have time to read the paper you sited above.

Good luck with the paper!

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