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

From: G908R NOD2 variant in a family with sarcoidosis

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 0.986a 0.972a STOPa 0.828a
SIFT 0.01 0a STOPa 0.05a
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
  1. 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