Table 3 Rare non-synonymous single-nucleotide variants and indels found in Maltese ALS patients.
From: Genetic analysis of ALS cases in the isolated island population of Malta
Prediction | Project MinE Allele Frequency | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
Gene | cDNA change | Protein change | dbSNP141 ID | MetaSVM | MetaLR | European gnomAD MAF | ALS cases | Controls | No. of patients | ALS type | Zygosity |
ALS2 | NM_020919.3:c.3206G>A | p.(Gly1069Glu) | rs200706696 | Damaging | Damaging | 0.0003 | 0.000376 | 0 | 1 | sALS | het |
ATXN2 | NM_002973.3:c.2950A>C | p.(Ile984Leu) | rs1338140819 | Tolerated | Tolerated | 0.00001 | NA | NA | 1 | sALS | het |
C21orf2 | NM_001271441.1:c.661G>A | p.(Ala221Thr) | rs746114248 | Tolerated | Tolerated | 0.0000 | NA | NA | 1 | sALS | het |
CAPN14 | NM_001145122.1:c.1249C>T | p.(Leu417Phe) | rs181906086 | Tolerated | Tolerated | 0.0183 | 0.004810 | 0.005259 | 1 | fALS | het |
DAO | NM_001917.4:c.250G>A | p.(Ala84Thr) | rs781658657 | Damaging | Damaging | 0.00001 | NA | NA | 2 | sALS | het |
DCTN1 | NM_004082.4:c.1484G>A | p.(Arg495Gln) | rs17721059 | Tolerated | Tolerated | 0.014 | 0.018945 | 0.019013 | 1 | fALS | het |
DCTN1 | NM_004082.4:c.586A>G | p.(Ile196Val) | rs55862001 | Tolerated | Tolerated | 0.0055 | 0.005720 | 0.006885 | 1 | sALS | hom |
DCTN1 | NM_004082.4:c.1864A>T | p.(Ile622Phe) | rs1328116832 | Damaging | Damaging | 0.00001a | NA | NA | 1 | sALS | het |
DDX20 | NM_007204.4:c.2237T>C | p.(Leu746Ser) | NA | Tolerated | Tolerated | NA | NA | NA | 1 | fALS | het |
DNAJC7 | NM_001144766.2:c.2T>C | p.(Met1?) | rs371236469 | Tolerated | Tolerated | 0.00005 | 0.000075 | 0 | 1 | sALS | het |
ERBB4 | NM_005235.2:c.3814G>A | p.(Gly1272Arg) | rs371332509 | Damaging | Damaging | 0.00001 | NA | NA | 1 | sALS | het |
ERBB4 | NM_005235.2:c.1122T>G | p.(His374Gln) | rs76603692 | Tolerated | Tolerated | 0.0009 | 0.001955 | 0.002429 | 1 | sALS | het |
ERBB4 | NM_005235.2:c.3176T>C | p.(Met1059Thr) | rs373685875 | Tolerated | Tolerated | 0.00001 | NA | NA | 1 | sALS | het |
EWSR1 | NM_013986.3:c.1798G>A | p.(Asp600Asn) | NA | Tolerated | Tolerated | NA | NA | NA | 1 | fALS | het |
EWSR1 | NM_013986.3:c.1408G>A | p.(Gly470Ser) | rs41311143 | Tolerated | Tolerated | 0.0121 | 0.013158 | 0.013754 | 1 | sALS | het |
GLE1 | NM_001003722.1:c.2078C>T | p.(Ser693Phe) | NA | Tolerated | Tolerated | NA | NA | NA | 1 | sALS | het |
KIF5A | NM_004984.2:c.2957C>T | p.(Pro986Leu) | rs113247976 | Tolerated | Tolerated | 0.018 | 0.020069 | 0.014777 | 1 | sALS | het |
MOBP | NM_001278322.1:c.586C>A | p.(Arg196Ser) | rs1188260744 | Tolerated | Tolerated | 0.0000 | NA | NA | 1 | sALS | het |
NEFH | NM_021076.3:c.2009T>A | p.(Val670Glu) | rs190692435 | Tolerated | Tolerated | 0.00676 | NA | NA | 2 | sALS, fALS | het |
NEK1 | NM_001199397.1:c.107A>G | p.(Asn36Ser) | rs1404362599 | Tolerated | Tolerated | NA | NA | NA | 1 | sALS | het |
SARM1 | NM_015077.4:c.1501T>C | p.(Tyr501His) | rs144613221 | Damaging | Tolerated | 0.00228 | 0.003458 | 0.002832 | 1 | sALS | het |
SCFD1 | NM_016106.3:c.209T>C | p.(Ile70Thr) | rs61754480 | Damaging | Damaging | 0.00403 | 0.004660 | 0.003843 | 1 | sALS | het |
SCFD1 | NM_016106.3:c.1297A>G | p.(Thr433Ala) | rs61754285 | Tolerated | Tolerated | 0.01788 | 0.018641 | 0.023058 | 2 | sALS | het |
SETX | NM_015046.5:c.7640T>C | p.(Ile2547Thr) | rs151117904 | Tolerated | Tolerated | 0.0032 | 0.007066 | 0.004652 | 1 | sALS | het |
SETX | NM_015046.5:c.2425A>G | p.(Ile809Val) | rs906452681 | Tolerated | Tolerated | 0.00003 | 0 | 0.000202 | 1 | sALS | het |
SETX | NM_015046.5:c.5308_5311del | p.(Glu1770Ilefs*15) | rs750959420 | Damagingb | Damagingb | 0.0000 | 0.000075 | 0 | 1 | sALS | het |
SPG11 | NM_025137.3:c.1618C>T | p.(Arg540Cys) | rs758046989 | Damaging | Damaging | 0.00001 | NA | NA | 1 | sALS | het |
SPG11 | NM_025137.3:c.6759C>G | p.(Asp2253Glu) | rs141818132 | Tolerated | Tolerated | 0.00003 | 0 | 0 | 1 | sALS | het |
SPG11 | NM_025137.3:c.1698T>G | p.(Asp566Glu) | rs79708848 | Tolerated | Tolerated | 0.01798 | 0.016165 | 0.014563 | 1 | sALS | het |
SPG11 | NM_025137.3:c.16G>A | p.(Gly6Arg) | rs200573434 | Tolerated | Tolerated | 0.00208 | 0.002330 | 0.001619 | 1 | sALS | het |
SPG11 | NM_025137.3:c.3037A>G | p.(Lys1013Glu) | rs111347025 | Tolerated | Tolerated | 0.01224 | 0.016912 | 0.017800 | 1 | sALS | het |
SPG11 | NM_025137.3:c.3425C>G | p.(Ser1142Cys) | rs201082396 | Tolerated | Tolerated | 0.0001 | NA | NA | 1 | fALS | het |
SPG11 | NM_025137.3:c.2656T>C | p.(Tyr886His) | rs139687202 | Tolerated | Tolerated | 0.0001 | 0.000225 | 0.000405 | 1 | sALS | het |
SPG11 | NM_025137.3:c.7256A>G | p.(Lys2419Arg) | rs76116949 | Tolerated | Tolerated | 0.0001 | 0.000075 | 0 | 1 | sALS | het |
TNIP1 | NM_001252390.1:c.437C>T | p.(Ala146Val) | rs2233289 | Tolerated | Tolerated | 0.0103 | 0.012103 | 0.013754 | 1 | sALS | het |
