The spectrum of rare variation in humans
Through interrogation of the gnomAD database (Karczewski, 2019) of publicly available exome and whole genome sequence, the number of synonymous (SYN), non-synonymous (NS), and loss-of-function (LOF) variants were tabulated (Figure 1, Supplemental Table 2 ). In addition, we determined the number of individuals homozygous for LOF variants and adjusted for gene size. The frequency of NS and LOF variants varies widely by gene. Therefore, this data can provide information on how essential a gene is by lower-than-expected levels of LOF mutations, rate of LOF variants per gene, and the ratio of NS/SYN variants. As expected, the essential, X-linked genes (ABCD1 ,ABCB7 ) and the essential ABCA3 and ABCE1 genes all have no or a deficient level of LOF variants and a low to very low ratio of NS/SYN variants.
Interestingly the ABCA2 , ABCB1 , ABCC5 , andABCG1 also have low levels of LOF variants, suggesting that they do not tolerate loss-of-function. Genes with a higher rate of NS and LOF variants include ABCC7/CFTR and ABCG2 . Several groups have proposed a heterozygous advantage for LOF alleles of CFTR to account for the high frequency of cystic fibrosis mutations in multiple populations (Angelicheva et al., 1994; Bosch et al., 2017; Prince, 1998). Furthermore, the increased blood uric acid levels in ABCG2 mutant carriers may also have a selective advantage against infectious diseases.
Analysis of specific predicted LOF mutations showed that all the cytoplasmic ABC genes (ABCE1 , ABCF1 , ABCF2 , andABCF3 ) have no reported homozygotes for LOF mutations, suggesting that they are essential. Similarly, almost all the half transporters (except for ABCB6 and ABCG2 ) also have no homozygous LOF individuals (Supplemental Table 2 ). In contrast, nearly half (46%) of all ABC full-transporters have at least 1 LOF allele reported to be homozygous in at least one individual (Figure 2 ). Interestingly some predicted LOF variants are frequent, including in some specific populations. For example, several genes in the ABCA5 gene cluster (ABCA6 , ABCA8 ,ABCA10 ) have common LOF alleles in Latin American and African populations. ABCA7 , ABCA13 , ABCB5 , ABCC11 , and ABCC12 also have specific common predicted LOF variants. Some of the predicted LOF alleles are in splice sites, and it may be that they can produce a functional protein by alternative splicing.