Table 1.
Rare (minor allele frequency <1%) GLE1 variations identified in ALS patients and controls
| Detected variants |
Frequency |
Prediction scores |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Exon | hg19/dbSNP | Coding DNA variant | Amino acid | FALS (n = 173) | SALS (n = 760) | Controls Sanger (n = 190) | Controls WES (n = 485) | Controls EVS (MAF %) | Grantham | GERP | |
| ALS only | 2 | g.131271264C>A | c.209C>A | p.S70X | 0 | 1 | 0a | 0 | No | NA | 3.650 |
| Intron 14 | g.131302552A>C | c.1965-2A>C | IVS14-2A>C | 1 | 0 | 0a | 0 | No | NA | 4.190 | |
| 16 | g.131303441C>T | c.2089C>T | p.R697C | 0 | 1 | 0a | 0 | No | 180 | 4.650 | |
| ALS and controls | 2 | g.131271171G>A RS138871311 | c.116G>A | p.C39Y | 0 | 1 | 2a | 1 | Yes (0.0581) | 194 | 4.350 |
| 7 | g.131287573G>A RS138310419 | c.1000G>A | p.E334K | 3 | 10 | 3 | 2 | Yes (1.0116) | 56 | 3.060 | |
| 13 | g.131300296G>T | c.1808G>T | p.R603L | 0 | 1 | 0a | 0 | Yes (0.0116) | 102 | 4.770 | |
| Controls only | 1 | g.131267089C>G RS150246404 | c.5C>G | p.P2R | 0 | 0 | 0 | 1 | Yes (0.0698) | 103 | 4.310 |
| 4 | g.131285910G>A | c.682G>A | p.V228M | 0 | 0 | 0 | 3 | No | 21 | −2.060 | |
| 6 | g.131287520G>A RS147943229 | c.947G>A | p.R316Q | 0 | 0 | 0 | 2 | Yes (0.1744) | 43 | 5.350 | |
| 7 | g.131287572C>G | c.999C>G | p.C333W | 0 | 0 | 1 | 0 | No | 215 | −3.330 | |
| 12 | g.131298693G>A RS121434407 | c.1706G>A | p.R569H | 0 | 0 | 1 | 2 | Yes (0.0465) | 29 | 5.920 | |
a
For these variations, 285 additional controls were tested by Sanger sequencing. Genomic positions are according to NM_001003722 from NCBI37/hg19 on the positive DNA strand. Reference SNP ID numbers (RS) were taken from the dbSNP database. Grantham matrix and GERP scores were obtained using SeattleSeq Annotation 137. FALS, familial amyotrophic lateral sclerosis; SALS, sporadic amyotrophic lateral sclerosis; WES, whole exome sequencing; EVS, Exome Variant Server (NHLBI GO Exome Sequencing Project, http://evs.gs.washington.edu/EVS/); MAF, minor allele frequency.