Table 3.

Characteristics of the segregating variants in P1 and P2.

Gene	Position	Ref.	Obs.	Protein	Polyphen-2	SIFT	CADD	ExAC allele counts	ExAC Z-score	ExAC pLI
COL9A3	chr20 61451333 (rs142639450)	G	A	NM_001853 c.G308A p.R103Q	0.022	0.31	23.5	Het: 1748, hom: 24 (119804); MAF: 0.01459	−1.09	0
HELZ2	chr20 62196625	G	A	NM_033405 c.G1843 p.E615K	0.809	0.84	0.002	Het: 78, hom: 1 (70806); MAF: 0.0011	0.25	0
RTEL1	chr20 62319010	G	T	NM_016434 c.G1368T p.W456C	1.000	0	28.8	Not observed	−1.71	0.78

Prediction scores were calculated with Polyphen-2 (42), SIFT (43), and CADD (44). Variant counts (in brackets: total analyzed alleles) and frequencies were downloaded from ExAC database (45) (accession date 21 February 2017) for the whole population.

Ref., reference; Obs., observed; het, heterozygous; hom, homozygous; pLI, probability of loss of function intolerance.