Table 1.

Prioritization of Variants in the Whole Exome Data from the Index Family

Filtering Criteria	Number of Remaining Variants
Total coding variants	31573
On removal of variants based on global minor allele frequency (MAF < 0.001) in 1000G, ExAC, Exome Variant Server, CG40, dbSNP, gnomAD browser	1320
On removal of variants based on population specific frequency (MAF < 0.001) in 1000G, ExAC, Exome Variant Server, gnomAD browser	850
Total number of protein disrupting variants (Synonymous variants removed)	605
Total number of homozygous variants shared among 3 affected (Exome sequenced)	0
Total number of heterozygous variants shared among 3 affected (Exome sequenced)	128
Total heterozygous variants present in all affected (Screened by target capture sequencing)	60
On removal of variants from regions with segmental duplication	45
On removal of >4 variants per gene	22
On removal of variants present in in-house control sample MAF > 0.001	15
Total number of variants segregating with the phenotype	2
Number of heterozygous segregating variants functionally relevant based on literature	2