G908R NOD2 variant in a family with sarcoidosis

Respiratory Research

Table 2 Description of heterozygous variants identified by whole-exome-sequencing in the family X

Gene variant	NOD2 2722G > C exon 8 NM_022162	IL17RA 958 T > C exon 11 NM_014339.6	KALRN 28C > T exon 1 NM_007064.3	EPHA2 2875G > A exon 17 NM_004431.3
Chr.	16	22	3	1
Position	50,756,540	17,586,757	124,303,696	16,451,766
QUAL	2521	3844	4578	10,401
Deph	278	370	528	618
rs ID number	rs2066845	rs140221307	rs56407180	rs139787163
Single nucleotide variant	missense	missense	nonsense	missense
PolyPhen2 prediction	0.986^a	0.972^a	STOP^a	0.828^a
SIFT	0.01	0^a	STOP^a	0.05^a
EXaC global MAF	0.009917	0.001801	0.002382	0.00346
Protein	NOD2 G908R	IL17RA W320R	–	EPHA2 A959T
Prior associations with disease	Crohn’s disease, Psoriatic arthritis, Blau syndrome	Familial Candidiasis	–	Age-related cortical cataract
Patient IB	Het	Het	Het	Het
Patient IIA	Het	Het	Het	Het
Patient IIB	Het	Het	Het	Het
Patient IIC	Het	A	A	A
Patient IID	A	A	A	A

Het heterozygous, A minor allele (C) absent, Chr chromosome, SNP single nucleotide polymorphism; Depth represents the number of reads identifying the SNP variant. QUAL., a quality parameter measuring the probability p that the observation of the variant is due to chance (for ex: QUAL = n, p = 1/n). It includes the DEPTH parameter and the coverage of the genomic sequence. The in silico functional evaluation of SNP variants was performed by using bioinformatics softwares SIFT, PolyPhen-2. The value indicating a putative pathogenic effect are near of 0 for SIFT and near of 1 for Polyphenv2, as indicated by the ^a. The minor allele frequency of SNP variants were evaluated by using the ExAC online database (http://exac.broadinstitute.org/). A global MAF including all ethnic origins lower than 0.01 suggest a rare variation and not a common polymorphism

ISSN: 1465-993X