Table 1. Putative loss of function variants across the family quartet.

	All variants		All rare/novel		Rare/novel and OMIM-disease associated gene
Variant type	HG19 reference (n = 4302405)	CEU reference (n = 3733299)	HG19 reference (n = 351555)	CEU reference (n = 354074)	HG19 reference	CEU reference
Coding-missense	9468	7982	1276	1276	203	200
Coding-nonsense	52	50	13	13	1	1
Coding-synonyn	11663	9928	1061	1059	186	186
Intronic	1303341	1128283	116276	115397	19544	19766
Splice-5′	156	147	16	16	0	0
Splice-3′	98	96	9	9	1	1
UTR-5′	40142	37794	3637	3619	510	516
UTR-3′	61826	59396	5989	5953	848	857
miRNA target	0	0	0	0	0	0
Pri-miRNA	2	2	1	1	0	0
Mature miRNA	0	0	0	0	0	0
Coding indels	1519	1476	432	412	73	71
Coding frameshift indels	440	418	273	253	29	27

Abbreviations: CEU reference, variant calls against CEU major allele reference; HG19 reference, variant calls against NCBI reference sequence 37.1; miRNA, micro RNA; Pri-miRNA, primary microRNA transcript; OMIM, Online Mendelian Inheritance In Man database; UTR, un-translated region.