Table 3. Exome Variant Summary.

	Average Autosomal Variants per Sample			Infantile parkinsonism-dystonia syndrome (n = 1)		Lethal neonatal rigidity and multifocal epilepsy (n = 2)		Microcephaly with chorioretinopathy (n = 1)		Non-syndromic mental retardation (n = 5)		Posterior column ataxia and retinitis pigmentosa (n = 1)		Symptomatic epilepsy and skull dysplasia (n = 3)		Usher syndrome (n = 2)
				Novel and Homozygous SNPs		SNPs in Mapped Interval		SNPs in Mapped Interval		SNPs in Mapped Interval		SNPs in Mapped Interval		SNPs in Mapped Interval		SNPs in Mapped Interval
	Total	Novel	Novel and Homozygous	Total	Linked Intervals	Total	Novel	Total	Novel	Total	Novel	Total	Novel	Total	Novel	Total	Novel
5′-Flanking	12	1	0
5′-UTR	25	0	0	1										1
3′-UTR	29	1	0
Intron	207	8	1									1				8
Missense	6,936	348	13	9		3		5		5	1	13	1	20	1	39	1
Nonsense	46	9	0													1
Read-through	10	1	0					1	1
Splice site	16	1	0	1	1
Synonymous	8,931	220	7	8		4		9		4		9		13		32
miRNA	5	1	0
IGR	56	1	0
Other	62	1	0
Indels *	203	75	*	*	*	2	1
Total	16,540	667	22	19	1	9	1	15	1	9	1	23	1	34	1	80	1

*Novelty for indels measured against dbSNP 129 only, automated indel caller does not determine zygosity.