Allelic frequencies (%) of recurrent variants in two JS and four non-JS cohorts
| JS | Non-JS | P value‡ | |||||
| European JS (n~551) | US JS (n~600) | WES-Mondino (n=987) | WES-OPBG (n=12 848) | NIG* (n~1685) | gnomAD† (n~1 25 000) | ||
| TMEM216 c.218G>T§ | 0.36 | 2.16 | 0.05 | 0 | 0 | 0.003 | p<0.00001 p<0.0001 |
| TMEM237 c.52C>T¶ | 0.18 | 0 | 0.05 | 0 | 0 | 0.006 | p<0.0001 ns |
| MKS1 c.1408–34_1408-6del** | 0.27 | 0.16 | 0.10 | 0.02 | 0 | 0.06 | p<0.005 ns |
| MKS1 c.1476T>G | 0.73 | 0.08 | 0 | 0.04 | 0.03 | 0.006 | p<0.00001 p<0.05 |
| KIAA0586 c.428delG | 2.27 | 3.26 | 1.06 | 0.44 | 0.84 | 0.31 | p<0.00001 ns |
| KIAA0586 exons8-10 del†† | 0.36 | 0.10 | n.a. | n.a. | n.a. | n.a. | - ns |
| KIAA0586 c.863_864delAA | 0.27 | 0.25 | 0 | 0 | 0 | 0.003 | p<0.00001 ns |
| KIAA0586 c.1006C>T | 0.18 | 0 | 0.05 | 0.008 | 0 | 0.0008 | p<0.00001 ns |
| RPGRIP1L c.1843A>C | 0.55 | 0.32 | 0 | 0.004 | 0 | 0.006 | p<0.00001 ns |
| CC2D2A c.4667A>T | 0.91 | 1.32 | 0.05 | 0.06 | 0.03 | 0.02 | p<0.00001 ns |
| TMEM67 c.755T>C | 0.27 | 0.16 | 0 | 0.008 | 0.06 | 0.008 | p<0.00001 ns |
*NIG: Network of Italian Genomes.
†gnomAD: genome aggregation database global frequencies (V.2.1.1). For the Ashkenazim and the Norther European/Finnish founder variants, the relative subpopulations have been excluded from gnomAD count to avoid an incorrect inflation of the control frequencies due to founder effect bias.
‡Upper line European JS versus all controls; lower line: European JS versus US JS. P values were calculated using χ2 test (with Fisher’s correction for TMEM237 c.52C>T and KIAA0586 c.1006C>T).
§Ashkenazi Jewish founder variant.
¶Hutterite founder variant.
**Finnish/Norther European founder variant.
††Being a large deletion, AF (alternative frequency) from non-JS cohorts are not available (n.a., not applicable).
JS, Joubert syndrome.