Table 3.

Functional heterozygous genetic variants with high predicted phenotypic effect at common variable immunodeficiency (CVID) candidate genes.

Patient	chr	Position	Gene	Function	Polyphen	rs	GERP	esp5400_all	HI1	HI2	RVIS	Essent
L294	chr9	100,774,719	ANP32B	Inframe indel	–	–	–	0	0.808	0.655	–0.16 (41.25%)	0.89
N214	chr7	2,976,742	CARD11	Missense	0.654	–	2.18	0	0.181	0.517	–1.39 (4.33%)	0.81
N212	chr11	60,892,540	CD5	Missense	0.936	–	3.08	0	0.284	0.402	0.8 (87.66%)	0.666
N232	chr1	160,523,750	CD84	Missense	0.999	rs146076557	5.25	0.000279	0.132	0.488	0.04 (57.15%)	0.077
L292	chr16	11,073,195	CLEC16A	Missense	0.857	rs74163607	5.3	0.000201	NA	0.578	–1.01 (8.2%)	0.547
N201	chr1	207,651,294	CR2	Missense	0.659	rs146465618	5.59	0.000093	0.234	NA	0.06 (57.56%)	0.558
N210	chr9	377,046	DOCK8	Missense	0.868	rs148693111	5.71	0.000186	0.535	0.57	–1.94 (1.9%)	0.845
L287	chr1	234,744,945	IRF2BP2	Inframe indel	–	–	2.62	0	0.852	0.626	–	0.992
N213	chr1	234,744,945	IRF2BP2	Inframe indel	–	–	2.62	0	0.852	0.626	–	0.992
N216	chr1	234,744,945	IRF2BP2	Inframe indel	–	–	2.62	0	0.852	0.626	–	0.992
L288	chr3	53,218,928	PRKCD	Missense	0.733	–	5.91	0	0.636	0.553	–1.04 (7.77%)	0.966

HI1 and HI2 haploinsufficiency predictions (24); RVIS, residual variation score of genetic variation intolerance (25) with the percentile of intolerant human genes in parentheses; Essent, essentiality index estimated from network and evolutionary properties (43).