Identification of novel candidate variants including COL6A6 polymorphisms in early-onset atopic dermatitis using whole-exome sequencing

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)

ISSN: 1471-2350