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

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

Base pair location in hg19 Variant type Nucleotide change Protein change phylop 1-sift PolyPhen2 Grantham score dbSNP137 Frequency in 1KG Project Casesa genotypes (homozygous reference allele, heterozygous, homozygous alternative allele) Controlsb 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 0.0020c
31778076 ns c.1674A > T p.Glu558Asp 0.108385 T B C . 0.0000089e 135,1,0 106,0,0 0.0020c
31779521 ns c.229G > A p.Gly77Ser 0.936178 D D MC rs368138379 0.0000770d 135,1,0 106,0,0 0.0020c
31778948 ns c.802G > A p.Ala268Thr 0.997482 D D MC rs34620296 0.0014000 134,2,0 106,0,0 0.0041c
31778950 ns c.800C > T p.Thr267Ile 0.998993 D D MC rs139868987 0.0014000 135,1,0 106,0,0 0.0020c
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 0.0000400e 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
  1. 14 variants ordered by variant type and within type ordered by frequency in 1000 Genome Project
  2. aSoton PIBD exomes, n = 136
  3. bSoton controls, n = 106
  4. cVariants used in the SKAT-O test
  5. dFrequency in NHLBI ESP
  6. eFrequency in ExAC Browser
  7. Dots denote missing data
  8. ns non-synonymous, sn synonymous, ifd in-frame deletion
  9. B benign, C conservative, D deleterious, MC moderately conservative, MR moderately radical, P possibly damaging, T tolerated