. 2022 Jun 23;53(5):640–656. doi: 10.1111/age.13233

TABLE 4.

Missense SNPs in genes of interest identified in chicken lines

SNP genome coordinate	Protein affected	Line(s) in which SNP is present	Alleles (ref/SNP)	Amino acid substitution	SIFT score	PROVEAN score	SNAP2 score	Comments on SNP location
Chr1:106,613,646	IFNAR1	6₁, 7₂, 0	G/A	A4T	0 ^b	0.012	−84
Chr1:106,613,656	IFNAR1	7₂	C/T	A7V	0 ^b	0.647	−25
Chr1:106,621,892	IFNAR1	15I, 6₁, 7₂, C, N, P2a ^a , 0, Wl	T/G	Y217D	0.29	0.363	32	Occurs in FN3 domain
Chr1:106,621,899	IFNAR1	N	A/G	E219G	0.44	−0.719	18	Occurs in FN3 domain
Chr1:106,623,894	IFNAR1	15I, 6₁, 7₂, C, N, 0, Wl	G/A	S324N	1	1.099	−81	Occurs in tissue factor domain
Chr1:106,625,990	IFNAR1	0 ^a	C/T	A404V	0.76	0.729	−87	Occurs in interferon binding domain
Chr1:106,587,598	IFNAR2	C	C/T	P45S	0 ^b	0.759	−78	Occurs in tissue factor domain
Chr1:106,588,380	IFNAR2	15I, 7₂, C, 0 ^a , Wl	C/T	H137Y	1	0.037	−65
Chr1:106,588,700	IFNAR2	15I, 7₂, P2a ^a , 0 ^a , Wl	A/G	N188D	0.7	−0.238	−89	Occurs in interferon binding domain
Chr1:106,589,401	IFNAR2	15I, P2a ^a , 0, Wl	T/C	I214T	0.11	−0.435	−68	Occurs in interferon binding domain
Chr1:106,589,970	IFNAR2	15I, C, P2a ^a , 0 ^a , Wl	G/T	G264V	0.15	0.584	−1	Occurs in transmembrane region
Chr1:106,590,778	IFNAR2	15I, C, P2a ^a , 0, Wl	A/G	I296V	1	−0.005	−75
Chr1:106,591,040	IFNAR2	15I, C, P2a ^a , 0 ^a , Wl	G/A	G383D	0.69	1.243	−29
Chr1:106,591,349	IFNAR2	15I, C, P2a ^a , 0, Wl	C/T	T486M	^aa0	−0.991	−62
Chr3:54,913,306	IFNGR1	15I, 6₁, 7₂, C, 0, Wl	T/C	V395A	0.27	−0.16	−16
Chr3:54,913,327	IFNGR1	15I, 6₁, 7₂, C, 0, Wl	G/A	R402Q	0.48	1.272	−71
Chr1:106,647,185	IFNGR2	6₁	T/C	C44R	0.62	3.391	−60	Occurs in tissue factor domain
Chr23:5,823,279	IFNLR1	N ^a	T/C	E151G	0 ^b	−1.341	−19	Occurs in interferon binding domain
Chr23:5,822,624	IFNLR1	C ^a	A/G	S199P	0.23	−1.046	14	Occurs in interferon binding domain
Chr23:5,822,588	IFNLR1	7₂ ^a , C ^a , 0 ^a	A/G	S211P	0.06	−4.218	41	Occurs in interferon binding domain
Chr1:106,602,130	IL10RB	6₁	T/G	S248A	1	0.375	−66
Chr1:106,603,837	IL10RB	6₁, 7₂, N, P2a ^a , 0 ^a	A/T	Q293H	0.04	−1.17	−95
Chr1:106,603,910	IL10RB	7₂	A/G	R318G	0.38	−0.716	9
Chr1:106,603,911	IL10RB	C, P2a ^a	G/A	R318K	1	−0.092	−78
ChrZ:7,372,479	IFNβ	N ^a	T/C	S151P	0.36	−1.728	52	Occurs in IFNα/β/δ domain
Chr7:7,923,855	STAT1	15I ^a , 7₂ ^a , Wl ^a	A/C	V341G	0.03 ^b	−4.766	39	Occurs in STAT binding domain
Chr8:28,566,979	JAK1	N ^a , P2a ^a , 0	A/G	V332A	0.67	−0.305	−67
Chr8:28,564,446	JAK1	C ^a , Wl ^a	A/C	Y500D	0.04	−3.757	61	Occurs in SH2 domain
Chr30:182,787	TYK2	7₂ ^a , Wl ^a	A/C	H215P	0.2	−2.732	63	Occurs in B41 domain
Chr30:183,686	TYK2	15I ^a , 6₁, 7₂, N, P2a, 0, Wl	G/A	R299Q	0.44	−0.551	−17	Occurs in B41 domain
Chr30:186,858	TYK2	7₂ ^a , C ^a , 0 ^a	T/C	V550A	0.01	−2.65	−26	Occurs in SH2 domain
Chr30:190,505	TYK2	6₁, 7₂, P2a, 0 ^a	G/A	S875N	0.45	0.351	−96	Occurs in TyrKc domain
Chr30:190,528	TYK2	C ^a	T/C	S883P	0.25	−3.994	12	Occurs in TyrKc domain
Chr30:190,801	TYK2	6₁ ^a	A/C	D908A	0.34	−1.029	−53
Chr20:10,064,956	IRF9	P2a ^a	T/C	H186R	0.51	−1.24	−38
Chr20:10,064,260	IRF9	6₁ ^a , C ^a , 0 ^a	T/G	Y355S	0.15	−4.102	63	Occurs in IRF‐3 domain

Scores in bold indicate a predicted significant effect.

^{^a}

SNP occurs in only one allele and is therefore heterozygous.

^{^b}

SIFT scores with low confidence in the value due to too few comparable sequences for the software to make a reliable prediction.