Table 3.
Targeted re-sequencing results for putative protective variants in CSMD1 (NC_000008.10) and PTPRD (NC_000009.11), detected only in controls
| Chr | Start | End | Ref | Alt | Gene | Exonic func. | AAChange | esp6500 | 1000g | snp138 | AC contr WGS | Freq | AC target | Freq target |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 8 | 2,807,805 | 2,807,805 | G | C | CSMD1 | Nonsynonymous | CSMD1:NM_033225:exon67:c.10262C>G:p.(Ala3421Gly) | NA | NA | NA | 1 | 0.0064 | NA | NA |
| 8 | 2,876,143 | 2,876,143 | G | A | CSMD1 | Nonsynonymous | CSMD1:NM_033225:exon52:c.7885C>T:p.(Pro2629Ser) | NA | NA | NA | 2 | 0.0128 | 3 | 0.0032 |
| 8 | 3,008,942 | 3,008,942 | C | G | CSMD1 | Nonsynonymous | CSMD1:NM_033225:exon40:c.6008G>C:p.(Arg2003Thr) | NA | NA | NA | 2 | 0.0128 | NA | NA |
| 8 | 3,165,321 | 3,165,321 | A | T | CSMD1 | Nonsynonymous | CSMD1:NM_033225:exon25:c.3846T>A:p.(His1282Gln) | NA | NA | NA | 1 | 0.0064 | NA | NA |
| 8 | 3,263,571 | 3,263,571 | G | A | CSMD1 | Synonymous | CSMD1:NM_033225:exon15:c.2244C>T:p.(Ser748=) | 0.0028 | 0.0028 | rs146267457 | 4 | 0.0256 | 5 | 0.0054 |
| 9 | 8,465,660 | 8,465,660 | A | T | PTPRD | Nonsynonymous | PTPRD:NM_001171025:exon14:c.2257T>A:p.(Ser753Thr),PTPRD:NM_001040712:exon15:c.2278T>A:p.(Ser760Thr),PTPRD:NM_130393:exon15:c.2272T>A:p.(Ser758Thr),PTPRD:NM_130391:exon16:c.2287T>A:p.(Ser763Thr),PTPRD:NM_130392:exon16:c.2287T>A:p.(Ser763Thr),PTPRD:NM_002839:exon32:c.3520T>A:p.(Ser1174Thr) | NA | NA | NA | 1 | 0.0064 | NA | NA |
| 9 | 8,485,810 | 8,485,810 | C | T | PTPRD | Nonsynonymous | PTPRD:NM_002839:exon28:c.3007G>A:p.(Gly1003Arg) | NA | NA | NA | 1 | 0.0064 | NA | NA |
| 9 | 8,486,142 | 8,486,142 | A | G | PTPRD | Nonsynonymous | PTPRD:NM_002839:exon28:c.2675T>C:p.(Val892Ala) | 0.0031 | 0.001 | rs151005956 | 1 | 0.0064 | 5 | 0.00543 |
| 9 | 8,486,278 | 8,486,278 | C | A | PTPRD | Nonsynonymous | PTPRD:NM_002839:exon28:c.2539G>T:p.(Val847Leu) | 0.0002 | NA | rs143787300 | 2 | 0.0128 | 2 | 0.00217 |
| 9 | 8,492,901 | 8,492,901 | C | A | PTPRD | Nonsynonymous | PTPRD:NM_002839:exon27:c.2428G>T:p.(Ala810Ser) | NA | NA | NA | 1 | 0.0064 | NA | NA |
Chr chromosome, Start start position, End end position, Ref reference allele, Alt alternative allele, Gene gene name, Exonic func. exonic function, AAChange amino-acid change, esp6500 frequency reported in the Esp6500 database, NA if variant is not reported, 1000g frequency reported in 1000 Genomes database, NA if variant is not reported, snp138 rs code if available, NA if rs code is not available, AC contr WGS allele count in the discovery cohort, Freq frequency in the discovery cohort, AC target allele count in the target sequencing cohort of 389 cases, NA if variant was not reported, Freq. target frequency in the target sequencing cohort of 389 cases, NA if variant was not reported