Table 2. Missense variants identified in individuals studied by WES.
| Patient code | |||
|---|---|---|---|
| 38-II-4, 38-II-5, 40-II-1, 40-II-3 | 54-II-2, 54-II-5 | 53-II-1 | |
| Chromosome and reference position (in hg19) | chr17:17701516(G) | chr2:26707436(C) | chr7:107350577(A) |
| Gene (exon) | RAI1 (exon 3) | OTOF (exon 12) | SLC26A4 (exon 19) |
| Nucleotide change (Amino acid change) | c.5254G>A (p.Gly1752Arg) * | c.1111C>G (p.Gly371Arg) * | c.2168A>G (p.His723Arg) |
| Accession number | NM_030665.3 | NM_194248.2 | NM_000441.1 |
| dbSNP138 (Global MAF) | rs755572135 (no info) ** | - | rs121908362 (G = 0.0004/1) |
| 1000 Genome Project database, alt. freq. | - | - | 0.0009 |
| Exome Sequencing Project (ESP) 6500 exomes | - | - | - |
| Exome Aggregation Consortium (ExAC): allele number (allele freq.) | 11: 107,784 (0.0001021) | - | 15: 121,166 (0.0001238) |
| PolyPhen2 HumVar score | 0.674 (possibly damaging) | 1.0 (probably damaging) | 1.0 (probably damaging) |
| SIFT | tolerated | damaging (0.0) | deleterious (0.0) |
| Mutation Taster | polymorphism | disease_causing (0.0) | disease_causing (0.0) |
| LRT | deleterious (0.000124) | deleterious (0) | deleterious (0) |
| PhyloP Score (100 vertebrates) | 1.308 | 7.701 | 6.299 |
* These sequence variants were submitted to ClinVar (http://www.ncbi.nlm.nih.gov/clinvar/) and the ClinVar accession numbers for the NM_030665.3: Chr.17_17701516_17701516_G_A and the NM_194248.2: Chr.2_26707436_26707436_C_G sequences are SCV000196150 and SCV000196151, respectively.
**—submitted by Genetic Services Laboratory, University of Chicago (Sept. 15, 2015).