Table 4.
Putatively functional SNPs in target SGS genes with significantly elevated minor allele frequency in Utah suicide cases
| Gene | SNP | Locationa | change | Sift/polyphen | ExAC Euro non-Finn freq (chroms)b | Suicide freq (chroms)c | p valued | Function; disease association |
|---|---|---|---|---|---|---|---|---|
| SP110 | rs181058279 | chr2: 231033860 | G:C; missense | Damaging; possibly damaging | 0.00006 (4/66714) | 0.0019 (5/2624) | 5.45E-06 | Gene transcription; [25] immune deficiency [31, 32] |
| AGBL2 | rs76215382 | chr11: 47711820 | G:A; missense | Damaging; probably damaging | 0.0148 (986/66668) | 0.0247 (65/2622) | 8.48E-05 | ATP/GTP binding; brain structure and function [33] |
| SUCLA2 | rs121908538 | chr13: 48528645 | A:G; missense | Damaging; probably damaging | 0.00003 (2/66524) | 0.0034 (9/2621) | 3.14E-12 | Mitochondrial protein, energy to synapse [34] |
| APH1B | rs745918508 | chr15: 63594615 | A; frameshift | LOF | 0.00007 (5/66712) | 0.0088 (23/2620) | 5.40E-29 | Transmembrane protein; Alzheimer’s [36]; and Parkinson’s [37] diseases |
aBase pair location hg19 genome build
bMinor allele frequency and number of chromosomes with the minor allele from European non-Finnish samples in the Exome Aggregation Consortium (ExAC) data
cMinor allele frequency and number of chromosomes with the minor allele derived from 1294–1312 Utah suicide cases with Illumina PsychArray data. For each variant, cases responsible for the original sharing were excluded. No case with a rare allele among those shown in this table had a known relationship (< 15th degree of relatedness) to the original high- risk family with SGS evidence
dComparison of UT suicide cases with the ExAC data; Fisher’s exact test used for rs181058279, rs121908538, and rs745918508; chi-square test used for rs76215382. P values exceed the significance threshold of 1.42E-04 correcting for 352 multiple tests