The role of admixture in the rare variant contribution to inflammatory bowel disease

Table 3 Mutability statistics for IBD loci

Gene	Age^a	EU RVIS^b	AA RVIS^b	pLI^c	LOEUF^d	pi_AA/pi_EU	pi_AA
Genes with elevated nucleotide diversity in Europeans
NOD2	679	1.88	-0.32	0	1.36	0.38	0.0003
DOK2	599	0.15	-0.40	0	1.07	0.53	0.0003
SLC93A8	1283	0.58	-0.25	0.67	0.47	0.56	0.0003
Genes with reduced nucleotide diversity in Europeans
CCR7	1029	-0.35	-0.44	0.06	0.78	4.08	0.0004
SDF2L1	690	n/a	n/a	0.19	0.95	4.73	0.0003
RELA	651	-0.61	-0.49	1	0.18	11.0	0.0001
Genes relatively tolerant of mutations
PTAFR	1508	-0.15	0.38	0.24	0.85	12.78	0.0002
HGFAC	1507	1.16	-0.09	0	0.87	1.06	0.0011
PDLIM5	480	1.68	0.82	0	0.55	0.83	0.0007
IL10RA	219	1.47	0.48	0.02	0.69	0.90	0.0009
Genes harboring protective rare variants
IL23R	2830	1.61	0.35	0	0.61	1.09	0.0005
TYK2	933	0.13	-0.78	0	0.56	0.69	0.0002
TAGAP	27,489	0.02	0.19	0.85	0.42	2.46	0.0001
CARD9	532	-0.58	-0.71	0	1.13	0.98	0.0007

^aFrom Human.Genome.Dating database, TMRCA point estimate in generation time for most common causal variant (first listed) in Table 1, using TGP datasource. 1000 generations correspond to 20,000–25,000 years
^bFrom RVIS database
^cFrom pLI database, inferred from European ancestry genomes
^dLOEUF score European estimates

ISSN: 1756-994X