Table 3.
Variants of uncertain significance found in spastic paraplegia probands
| Patient ID | Gene | Chr | Genomic position | cDNA change | Allele zygocity | PhyloP score | ClinVar | SIFT/PolyPhen/MutTaster | ExAC allele frequency† | rs number | Inheritance |
|---|---|---|---|---|---|---|---|---|---|---|---|
| SPG0403 | WASHC5 | 8 | g.126091044 | NM_014846.3:c.647C>T | ht | 5443 | na | tol/pb_dam/dc | 0.001694 (0.00122) | rs72720524 | AD |
| NP_055661.3:p.(Pro216Leu) | |||||||||||
| SPG1402 | KIF5A | 12 | g.57965883 | NM_004984.2:c.1402C>T | ht | 1.19 | na | del/bn/dc | 0 (0.0000084) | rs771021589 | AD |
| NP_004975.2:p.(Arg468Trp) | |||||||||||
| SPG0303 | ITPR1 | 3 | g.4716885 | NM_001168272.1:c.2687C>T | ht | 1719 | us | tol/bn/dc | 0.00051 (0.000315) | rs201519806 | AD |
| NP_001161744.1:p.(Ala896Val) | |||||||||||
| SPG0401 | ITPR1 | 3 | g.4716885 | NM_001168272.1:c.2687C>T | ht | 1719 | us | tol/bn/dc | 0.00051 (0.000315) | rs201519806 | AD |
| NP_001161744.1:p.(Ala896Val) | |||||||||||
| SPG1203 | ITPR1 | 3 | g.4725441 | NM_001168272.1:c.3412A>G | na | 4274 | us | tol/bn/dc | 0.0008452 (0.000484) | rs199698357 | AD |
| NP_001161744.1:p.(Met1138Val) | |||||||||||
| g.4821291 | NM_001168272.1c.6304G>T | 4331 | del/bn/dc | 0.000105 (0.000058) | rs373973399 | ||||||
| NP_001161744.1:p.(Ala2102Ser) | |||||||||||
| SPG0503 | SETX | 9 | g.135140243 | NM_015046.5:c.7417C>G | ht | 3436 | na | tol/ps_dam/pol | 0 (0.000033) | rs760196991 | AD |
| NP_055861.3:p.(Leu2473Val) |
† according European (non-Finnish) population, total frequency in bracket
bn benign, dc disease causing, del deleterious, ht heterozygous, na not applicable, pb_dam probably damaging, pol polymorphism, ps_dam possibly damaging, rs reference SNP, tol tolerated, us uncertain significance