Fig. 3: Loss of function mutations.
From: South Asian medical cohorts reveal strong founder effects and high rates of homozygosity
a Number of high confidence loss of function genes found at a minimum of 0.1% MAF in their relative population for overall non-Finnish European (NFE), NFE and not in SAS (NFE Unique), NFE and SAS (NFE and SAS), SAS and not NFE (SAS Unique) and overall for SAS. b Loss of function gene space by population. Each square represents a distinct gene and is colored by its maximum AF within the relative group. Genes are separated by groups in which they are found (from top to bottom and then left to right): NFE unique, NFE and SAS, PKN unique, PKN and SOI, PKN and BNG, all of SAS (PKN and SOI and BNG), SOI unique, BNG unique, and BNG and SAS. c Effects of pLoF variants on blood lipid markers replicated the known biology: PCSK9 pLoFs associated with decreased LDL, ANGPTL3 pLoFs associated with decreased triglycerides, and CETP pLoF associated with increased HDL. Only samples from South India (Bangalore and Chennai) were included. P values were calculated using the Wilcoxon rank-sum test. Box shows median and middle 50% of the distribution; whiskers show values within 1.5 times the interquartile range from the first and third quartiles. d Mean number of homozygous pLoF variants per individual, stratified by population and estimated degree of inbreeding. e APOC3 p.Arg19Ter alleles are found at a high frequency among Balochi and Sindhi individuals from Southern Pakistan. Three of the self-reported Balochis and Sindhis were heterozygous carriers, but a larger number of carriers without self-reported identity were mapped to the same region on the UMAP plot.
