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 | 0.986a | 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 |
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