Table 3.

Family-specific common and rare variants in Family A

	Common variant						Functional prediction program
Gene	RS#	aChr	bPOS	cAmino acid change	Type	dSIFT	ePolyphen2	fPhyloP	gPhastCons	hGlobal	East Asian	iKorean
COL6A6	16830494	chr3	130,361,856	R1739Q	cSNP	0.04	0.272	1.703	0.995	0.12	0.19	0.188
ANKRD35	11579366	chr1	145,562,293	E661Q	cSNP	0.38	0.971	5.285	1	0.39	0.26	0.233
TUFT1	3828054	chr1	151,512,895	Q18R	cSNP	0.77	0.688	1.688	0.288	0.1	0.03	0.047
TMEM175	34311866	chr4	951,947	M393T	cSNP	0.01	0	1.299	0.999	0.12	0.12	0.155
EDN1	5370	chr6	12,296,255	K198N	cSNP	0.08	0.454	0.049	0.001	0.21	0.28	0.258
NRAP	2270182	chr10	115,392,919	N519I	cSNP	0.19	0.958	2.477	1	0.26	0.20	0.205
HGFAC	16844401	chr4	3,449,652	R509H	cSNP	0.22	0.943	2.662	0.593	0.07	0.10	0.115
UNC93A	2235197	chr6	167,709,702	W151	STOP GAINED	.	.	4.525	1	0.1	0.15	0.163
ABCA13	1771229	chr7	48,313,881	F1540L	cSNP	.	0.997	2.325	0.614	0.11	0.17	0.255
SSPO	1005603	chr7	149,516,881	S4028I	cSNP	.	.	.	.	0.2	0.19	0.181
TTC40	12781609	chr10	134,748,331	S264N	cSNP	.	.	.	.	0.37	0.36	0.412
Rare variant
DNAH17	.	chr17	76,567,792	I204M	cSNP	0.11	.	1.926	0.992	.		.
COL6A6	200963433	chr3	130,289,976	R906C	cSNP	0	1	4.596	1	0.0014	0.01	0.017

^aChr = Chromosome

^bPos = Position

^cAmino acid changes = single-letter codes for amino acids are presented, cSNP = single-nucleotide polymorphisms in coding regions

^dSIFT, prediction scores for amino acid substitutions that affect protein function (damaging < 0.05, tolerance > 0.05; scores range from 0 to 1)

^ePolyphen2, prediction of the possible impact of amino acid substitutions (0.957 < probably damaging < 1, 0.453 < possibly damaging < 0.956, 0 < benign < 0.452; scores range from 0 to 1)

^fPhyloP, prediction of conserved sites across species; a higher score indicates a more conserved site (values > 0)

^gPhastCons, predicts the possibility that a nucleotide belongs to a conserved element in the phylogenetic tree (Values > 0.2)

^hGlobal frequency, variants with MAFs as low as 1% or with an unknown frequency (value < 0.01)

ⁱKorean frequency, variants with MAFs as low as 2% or in unknown genes (values > 0.02)