S.No
Location
Nucleotide change
dbSNP ID
General
General
Functional
Functional
Conservation
Conservation
PolyPhen-2
I Mutant v2.0
Consurf Score
VarSome (ACMG guidelines)
DANN
Mutation taster
SIFT
Provean
LRT
Mutation Assessor
Missense variants Missense variants Missense variants Missense variants Missense variants Missense variants Missense variants Missense variants Missense variants Missense variants Missense variants Missense variants Missense variants Missense variants
1 GNPTAB c.3598G>A rs137853825 0.9982 Disease causing D Damaging Deleterious Low PD Decreased stability 9 Likely Benign
2 GNPTG c.802A>C rs759796840 0.9696 Disease causing D Neutral Deleterious Medium PD Decreased stability 8 VUS
3 NAGPA c.131G>C rs374266430 0.9819 Polymorphism D Damaging Neutral Medium PD Decreased stability 4 VUS
4 NAGPA c.139C>T rs371054576 0.8056 Polymorphism T Neutral Neutral Neutral B Decreased stability 1 VUS
5
NAGPA
c.1394 C>T
rs7188856
0.3973
Polymorphism automatic
T
Neutral
Neutral
Low
PD
Decreased stability
1
Benign
Synonymous variants Synonymous variants Synonymous variants Synonymous variants Synonymous variants Synonymous variants Synonymous variants Synonymous variants Synonymous variants Synonymous variants Synonymous variants Synonymous variants Synonymous variants Synonymous variants
6 GNPTAB c.1932A>G rs10778148 0.4236 - - - - - - - - Benign
7 GNPTG c.702T>C rs532275192 0.3353 - - - - - - - - VUS
8 GNPTG c.813G>A rs377647926 0.4781 - - - - - - - - VUS
9 NAGPA c.333 G>A rs2972272 0.5259 - - - - - - - - Benign
10 NAGPA c. 1485C>T rs887854 0.7803 - - - - - - - - Benign
Non coding variants Non coding variants Non coding variants Non coding variants Non coding variants Non coding variants Non coding variants Non coding variants Non coding variants Non coding variants Non coding variants Non coding variants Non coding variants Non coding variants
11 GNPTG -4 C>T rs554707396 0.9074 - - - - - - - - VUS
12 NAGPA c.1174+53C>A rs2937112 0.7424 - - - - - - - - Benign