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Table 3 Pathogenic and likely pathogenic variants observed in the three commonest disorders

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 no. Number of Variants Variant description:
cDNA position
Protein change
ACMG criteria No of individuals
1 Deafness, AR 4, with enlarged vestibular aqueduct, SLC26A4 ENST00000265715 4 c.1001G > T, p.Gly334Val PS3 + PM2 + PP2 + PP3 + PP4 + PP5 2
c.1226G > C, p.Arg409Proa PM2 + PM5 + PP2 + PP3 + PP5 1
c.1468A > C, p.Ile490Leua PS1 + PM1 + PP2 + PP3 + PP5 1
c.1003 T > C, p.Phe335Leu PS1 + PP2 + PP3 + PP5 1
2 Deafness, AR,1A, GJB2 ENST00000382844 2 c.231G > A, p.Trp77Tera PVS1 + PS3 + PM1 + PM4 + PP2 + PP3 2
c.71G > A, p.Trp24Tera PVS1 + PS3 + PM1 + PM4 + PP2 + PP3 1
3 Deafness, AR, 8, TMPRSS3 ENST00000291532 2 c.413C > A, p.Ala138Glu PM1 + PM2 + PP2 + PP3 1
c.323-6G > Aa PS3 + PS4 + PM2 + PP3 2
4 Deafness AR,7, TMC1 ENST00000297784 1 c.1165C > T, p.Arg389Ter PVS1 + PS3 + PM2 + PM4 + PP3 1
5 Cystic fibrosis, CFTR ENST00000003084 9 c.223C > T, p.Arg75Ter PVS1 + PS3 + PM2 + PM4 + PP2 + PP3 1
c.1646G > A, p.Ser549Asna PS3 + PM1 + PM2 + PM5 + PP2 + PP3 + PP5 1
c.595C > T, p.His199Tyr PS3 + PM1 + PM2 + PM5 + PP2 + PP3 + PP5 1
c.3209G > A, p.Arg1070Gln PS3 + PM1 + PM5 + PP2 + PP3 + PP5 1
p.Phe508del PS3 + PM1 + PM4 + PP2 + PP3 1
c.4096A > T, p.Ile1366Phe PM1 + PM2 + PP2 + PP3 1
c.1472G > T, p.Cys491Phe PM1 + PM2 + PP2 + PP3 1
c.4009 T > G, p.Phe1337Val PM1 + PM2 + PP2 + PP3 1
c.1859A > T, p.His620Leu PM1 + PM2 + PM5 + PP2 + PP3 1
6 Glycogen storage disease II, GAA ENST00000302262 1 c.1933G > A, p.Asp645Asn PS4 + PM1 + PM2 + PM5 + PP2 + PP3 + PP5 3
  1. PVS Pathogenic very strong, PS Pathogenic strong, PM pathogenic moderate, PP Pathogenic supporting [51] (Supplementary file 3), adescribed from the Indian subcontinent