Table 2.

Prioritization of Variants Identified by Exome Sequencing of DNA from Subject J-6

	Total	Within Regions of Homozygositya	Within Regions of Homozygosity Shared among Affected but Not Unaffected Siblingsb
All variants	15,611	1,223	81
Only NS/SS/I,	7,247	588	40
AND ≤ 0.5% MAF in 1000 genomes,	648	41	3
AND ≤ 0.5% MAF in internal database	580	36	3
AND are predicted to be loss of function	80	7	0

Variants presented were sequentially filtered on the basis of effect on protein sequence (synonymous or intronic variants were excluded), presence in the 1000 Genomes Project dataset (with ≤ 0.5% MAF; the 20101123 sequence and alignment release including 1094 individuals was used), presence in exomes from an internal database (with ≤ 0.5% MAF; DNA from 224 samples processed with the same tools as J-6), and being presumed to cause loss of protein function (nonsense, splice site variants and frameshifting insertions-deletions).

Abbreviations are as follows: SNP, single-nucleotide polymorphism; NS/SS/I, nonsynonymous, splice site or coding insertion-deletion variants; and MAF, minor-allele frequency.

^aBased on exome sequencing data.

^bbased on SNP genotyping data.