Table 2. Ethnic-specific MAF and in silico pathogenicity prediction of CDH23 variants in our study.
Variant | Patient | dbSNP | In-house exome from KNIH (n = 700) | KRG database (n = 622) | Genotyping (n = 384) | SGI (n = 1020) | Score in Pph2/ SIFT/ GERP | MAF in composite cohort | ExAC | 1000 Genomes |
---|---|---|---|---|---|---|---|---|---|---|
p.T1618K (c.C4853A) | SH59-133 (Pediatric) | No data | 0/1400 | Not detected in unknown number | 0/768 | 0/2040 | Probably Damaging/ Damaging / 5.9 | 0% (0/4208) | N/A | N/A |
p.P240L (c.C719T) | SH59-133 SH151-324 SB116-208 (Pediatric & Adult) | rs121908354 (flagged) | 1/2040 | Possibly Damaging/ Damaging/ 5.19 | 0.05% (1/2040) | 0.00009 | 0.0002 | |||
p.D2202N (c.G6604A) | SH62-147 (Adult) | rs121908349 (flagged) | 0/1400 | Not detected in unknown number | 0/768 | 0/2040 | Probably Damaging/ Damaging/ 5.06 | 0% (0/4208) | 0.000008 | N/A |
p.A1713D (c.C5138A) | SB210-412 (Adult) | No data | 0/2040 | Probably Damaging/ Damaging/ 5.4 | 0% (0/2040) | N/A | N/A | |||
p.P402L (c.C1205T) | SB210-412 (Adult) | rs373168635 (Non-flagged) | 0/2040 | Probably Damaging/ Tolerated/ 4.91 | 0% (0/2040) | 0.00003 | N/A | |||
p.R1588W (c.C4762T) | SH151-324 (Adult) | rs137937502 | 4/1400 | 2/1244 | 1/768 | 1/2040 | Probably Damaging/ Damaging/ 3.24 | 0.15% (8/5452) | 0.0002 | 0.0008 |
p.R1916H (c.G5747A) | SH62-147 (Adult) | rs746971522 | 3/1400 | 2/518 | 0/764 | 0/2040 | Probably Damaging/ Damaging/ 4.28 | 0.11% (5/4722) | 0.00006 | N/A |
KRG, Korean Reference Genome (http://152.99.75.168/KRGDB); ExAC, Exome Aggregation Consortium (http://exac.broadinstitute.org/); 1000 Genomes (https://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/); N/A, not applicable