Table 1.
Rare gene variants identified in the “independent PS control group”
| Gene | Position (hg19) | Ref | Alt | MAF | Variants | dbSNP id | Freq |
Pathogenicity |
|
|---|---|---|---|---|---|---|---|---|---|
| GERP | POLYPHEN2 prediction | ||||||||
| HRASLS5 |
chr11:63,230,659 |
G |
C |
0.040 |
Intron_variant |
rs2282479 |
0.017 |
1.14 |
Unknown |
| HRASLS5 |
chr11:63,233,710 |
A |
G |
0.189 |
Leu207Leu |
rs2275999 |
0.100 |
4.16 |
Unknown |
| HRASLS5 |
chr11:63,256,441 |
C |
G |
0.207 |
Ala93Pro |
rs940611 |
0.033 |
−1.03 |
Benign (0.000) |
| HRASLS5 |
chr11:63,258,424 |
C |
T |
unknown |
Arg28Gln |
unknown |
0.017 |
−5.14 |
Poss-dam (0.897) |
| LGALS12 |
chr11:63,276,480 |
G |
A |
0.023 |
Intron_variant |
rs200256001 |
0.033 |
−2.69 |
Unknown |
| LGALS12 |
chr11:63,277,334 |
A |
G |
0.009 |
Ile176Val |
rs117587231 |
0.017 |
4.42 |
Benign (0.005) |
| LGALS12 |
chr11:63,278,621 |
C |
G |
0.333 |
Intron_variant |
rs2239679 |
0.200 |
−0.07 |
Unknown |
| PLA2G16 | chr11:63,381,458 | C | T | 0.072 | Intron_variant | rs61929725 | 0.150 | −5.26 | Unknown |
Variant location is reported using hg19 coordinates. MAF, minor allele frequency according to the NCBI dbSNP137 database; Freq, frequency of the variant allele in the cohort of 30 patients; GERP, Genomic Evolutionary Rate Profiling; the POLYPHEN2 measures of pathogenicity are: Benign, possibly damaging (Poss-dam), and probably damaging based on the false discovery rate.