Table 2.
Prioritized Rare Recessive Variants Present in Subject 3
| Gene | Type | Exon | Effect | HGVS Genomic Change (GenBank ID) | cDNA | Protein | CADD Phred Score |
|---|---|---|---|---|---|---|---|
| THUMPD2 | SNV | 3 | MS | g.39996996C>A (NC_000002.11) | c.526G>T | p.Asp176Tyr | 25.4 |
| NBEAL2 | SNV | 32 | MS | g.47043984C>T (NC_000003.11) | c.5275C>T | p.Arg1759Cys | 26.8 |
| RNF123 | SNV | 24 | MS | g.49743006G>A (NC_000003.11) | c.2198G>A | p.Arg733Gln | 24.4 |
| IFRD2 | SNV | 2 | MS | g.50328075T>C (NC_000003.11) | c.286A>G | p.Ser96Gly | 25.4 |
| CACNA2D3 | SNV | 9 | MS | g.54615858C>G (NC_000003.11) | c.917C>G | p.Pro306Arg | 31 |
| IL17RD | SNV | 10 | MS | g.57136593A>G (NC_000003.11) | c.893T>C | p.Ile298Thr | 28.4 |
| MYLK | SNV | 23 | SP | g.123382947C>A (NC_000003.11) | c.3985+5G>T | – | 21.4 |
| SEC24D | SNV | 2 | SP | g.119754899C>T (NC_000004.11) | c. −41−7G>A | – | 9.701 |
| SLC26A5 | SNV | 16 | MS | g.103019758T>C (NC_000007.13) | c.1609A>G | p.Ile537Val | 23.6 |
| CNTLN | SNV | 22 | SP | g.17465974T>C (NC_000009.11) | c.3532−5T>C | – | 12.13 |
| EHMT1 | SNV | 12 | S | g.140671136C>A (NC_000009.11) | c.1858C>A | – | 20.8 |
| SIGLEC1 | Del | 21 | F | g.3669236delT (NC_000020.10) | c.5101delA | p.Thr1701Profs∗26 | 33 |
Abbreviations are as follows: SNV, single-nucleotide variant; MS, missense variant; F, frameshift variant; S, synonymous variant; and SP, putative splice variant.