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Table 4 Pathogenic and likely pathogenic variants in other genes

From: NGS-based expanded carrier screening for genetic disorders in North Indian population reveals unexpected results – a pilot study

S. no Disorder and Gene Transcript Number of variants Variant description: cDNA position
Protein change
ACMG criteria No of individuals
1 Methylmalonic aciduria, cbla type, MMAA ENST00000281317 1 c.433C > T
p.Arg145Ter
PVS1 + PS3 + PM4 + PP2 + PP3 2
2 Epidermolysis bullosa dystrophica, AR, COL7A1 ENST00000328333 1 c.5287C > T
p.Arg1763Ter
PVS1 + PM1 + PM4 + PP2 1
3 Galactosemia, GALT ENST00000378842 1 c.563A > G
p.Gln188Arg
PS3 + PM1 + PP2 + PP3 + PP4 + PP5 2
4 Smith-Lemli-Opitz syndrome, DHCR7 ENST00000355527 2 c.730G > A
p.Gly244Arg
PS1 + PM2 + PP2 + PP3 + PP4 + PP5 1
5 c.862G > A
p.Glu288Lys
PM2 + PP1 + PP2 + PP3 + PP4 + PP5 1
6 Biotinidase deficiency, BTD ENST00000303498 1 c.469C > T
p.Arg157Cys
PS3 + PM1 + PM2 + PM5 + PP2 + PP3 1
7 Medium chain ACYL-CoA dehydrogenase deficiency, ACADM ENST00000420607 1 c.811G > G/A
p.Gly271Arg
PS1 + PS3 + PP2 + PP3 + PP5 1
8 Junctional Epidermolysis bullosa, LAMB3 ENST00000391911 1 c.2138-2A > Ga PVS1 + PM2 + PP3 2
9 Metachromatic leukodystrophy, ARSA ENST00000216124 1 c.1210 + 1G > Ta PVS1 + PM2 + PP3 + PP5 1
10 Peroxisome biogenesis disorder 1A (Zellweger), PEX1 ENST00000248633 1 c.2926 + 2 T > C PVS1 + PM2 + PP3 + PP5 1
11 Polycystic kidney disease, AR, PKHD1 ENST00000371117 2 c.8441-1G > Ca PVS1 + PM2 + PP3 1
12   c.1480C > T, p.Arg494Ter PVS1 + PS3 + PM2 + PM4 + PP2 1
13 Albinism type 2, OCA2 ENST00000354638 1 c.1580 T > G
p.Leu527Argb
PM2 + PP2 + PP3 + PP4 + PP5 2
14 Phenylketonuria, PAH ENST00000553106 1 c.688G > A
p.Val230Ile
PS4 + PM1 + PP2 + PP3 + PP5 2
15 Limb Girdle muscle dystrophy type 2A, CAPN3 ENST00000397163 1 c.1504A > G
p.Ile502Val
PM1 + PM2 + PM5 + PP2 + PP3 1
16 Congenital adrenal hyperplasia, CYP21A2 ENST00000418967 1 c.373C > T
p.Arg125Cys
PM2 + PP2 + PP3 + PP4 + PP5 1
17 Megalencephalic leukoencephalopathy with subcortical cysts, MLC1 ENST00000311597 2 c.65G > A
p.Arg22Gln
PS3 + PP2 + PP3 + PP4 1
18   c.959C > A
p.Thr320Lys
PS3 + PM2 + PP2 + PP3 + PP5 1
19 Primary hyperoxaluria type 1, AGXT ENST00000307503 1 c.302 T > C
p.Leu101Prob
PS3 + PM2 + PP2 + PP3 1
20 Gaucher disease, GBA ENST00000327247 2 c.866G > C
p.Gly289Alab
PM2 + PP2 + PP3 + PP4 + PP5 1
21 c.1448 T > C
p.Leu483Prob
PS3 + PM5 + PP2 + PP3 + PP5 1
22 Argininosuccinic aciduria, ASL ENST00000304874 1 c.857A > G
p.Gln286Arg
PS4 + PP2 + PP3 + PP5 1
23 Canavan disease, ASPA ENST00000263080 1 c.902 T > C
p.Leu301Prob
PM2 + PP2 + PP3 + PP4 + PP5 1
24 Glutaric acidemia type 1, GCDH ENST00000222214 1 c.281G > A
p.Arg94Glnb
PM2 + PM5 + PP2 + PP3 + PP4 + PP5 1
25 Krabbe disease, GALC ENST00000261304 1 c.956A > G
p.Tyr319Cysb
PM1 + PM2 + PM5 + PP2 + PP3 1
26 Congenital ichthyosis, AR 1, TGM1 ENST00000206765 1 c.550C > T
p.Pro184Ser
PM2 + PM3 + PP2 + PP3 + PP5 1
27 Very Long chain fatty acid acyl-CoA dehydrogenase deficiency, ACADVL ENST00000543245 1 c.1480 T > C
p.Phe494Leu
PM1 + PM2 + PP2 + PP3 1
28 Niemann Pick disease type C1, NPC1 ENST00000269228 1 c.3560C > T
p.Ala1187Val
PM5 + PP2 + PP3 + PP4 + PP5 1
  1. PVS – pathogenic very strong, PS – pathogenic strong, PM– pathogenic moderate, PP – pathogenic supporting [51] (Supplementary file 3), aNovel variant, bdescribed from the Indian subcontinent