De novo and rare mutations in the HSPA1L heat shock gene associated with inflammatory bowel disease

Table 2 Variants found in patients with IBD and controls in HSPA1L (no filtering applied)

Base pair location in hg19	Variant type	Nucleotide change	Protein change	phylop	1-sift	PolyPhen2	Grantham score	dbSNP137	Frequency in 1KG Project	Cases^a genotypes (homozygous reference allele, heterozygous, homozygous alternative allele)	Controls^b genotypes (homozygous reference allele, heterozygous, homozygous alternative allele)	MAF within combined cases and controls cohort
31779233	ifd	c.515_517del	p.Leu172del	.	.	.	.	.	.	135,1,0	106,0,0	0.0020^c
31778076	ns	c.1674A > T	p.Glu558Asp	0.108385	T	B	C	.	0.0000089^e	135,1,0	106,0,0	0.0020^c
31779521	ns	c.229G > A	p.Gly77Ser	0.936178	D	D	MC	rs368138379	0.0000770^d	135,1,0	106,0,0	0.0020^c
31778948	ns	c.802G > A	p.Ala268Thr	0.997482	D	D	MC	rs34620296	0.0014000	134,2,0	106,0,0	0.0041^c
31778950	ns	c.800C > T	p.Thr267Ile	0.998993	D	D	MC	rs139868987	0.0014000	135,1,0	106,0,0	0.0020^c
31779728	ns	c.22G > C	p.Ala8Pro	0.995889	D	D	C	rs9469057	0.0130000	136,0,0	103,3,0	0.0061
31778077	ns	c.1673A > C	p.Glu558Ala	0.995982	T	P	MR	rs2227955	0.0480000	129,7,0	98,8,0	0.0309
31777946	ns	c.1804G > A	p.Glu602Lys	0.997651	D	B	MC	rs2075800	0.2900000	57,57,22	48,49,9	0.3471
31778272	ns	c.1478C > T	p.Thr493Met	0.008994	T	B	MC	rs2227956	0.8800000	6,33,97	2,23,81	0.1487
31778697	sn	c.1053G > C	p.Leu351Leu	.	.	.	.	rs199780750	0.0000400^e	135,1,0	106,0,0	0.0020
31779003	sn	c.747G > A	p.Arg249Arg	.	.	.	.	rs116768554	0.0027000	135,1,0	106,0,0	0.0020
31778322	sn	c.1428C > T	p.Ile476Ile	.	.	.	.	rs35347921	0.0040000	135,1,0	106,0,0	0.0020
31778831	sn	c.919 T > C	p.Leu307Leu	.	.	.	.	rs35326839	0.0200000	133,3,0	102,4,0	0.0144
31778529	sn	c.1221G > A	p.Thr407Thr	.	.	.	.	rs2075799	0.1400000	123,13,0	90,14,2	0.0640

14 variants ordered by variant type and within type ordered by frequency in 1000 Genome Project
^aSoton PIBD exomes, n = 136
^bSoton controls, n = 106
^cVariants used in the SKAT-O test
^dFrequency in NHLBI ESP
^eFrequency in ExAC Browser
Dots denote missing data
ns non-synonymous, sn synonymous, ifd in-frame deletion
B benign, C conservative, D deleterious, MC moderately conservative, MR moderately radical, P possibly damaging, T tolerated

ISSN: 1756-994X