Table 3 In silico prediction of exonic variants observed in the HBD gene in the Iranian population, based on the Iranome project (http://www.iranome.ir/)
From: In silico prediction of HBD gene variants in the Iranian population
Tool | c.394C>G/p.Gln132Glu | c.159 T>G/p.Asp53Glu | c.90C>T/p.Gly30= | c.49G>C/p.Gly17Arg | c.14C>T/p.Thr5Ile | c.294C>T/p.His98= | c.82G>T/p.Ala28Ser |
|---|---|---|---|---|---|---|---|
MutationTaster | Disease causing | Polymorphism | Disease causing | Polymorphism | Polymorphism | Disease causing | Disease causing |
SIFT | Tolerated | Tolerated | Tolerated | Deleterious | Deleterious | Tolerated | Tolerated |
PROVEAN | Neutral | Neutral | Neutral | Deleterious | Deleterious | Neutral | Neutral |
PolyPhen-2 | Benign | Benign | NA | Benign | Possibly damaging | NA | Possibly damaging |
FATHMM-XF | Pathogenic | Benign | Benign | Benign | Benign | Benign | Benign |
I-Mutant Disease | Disease | Neutral | NA | Disease | Neutral | NA | Neutral |
SNPs&GO | Neutral | Neutral | NA | Disease | Neutral | NA | Neutral |
CADD | 18.06 | 11.91 | 23.5 | 0.904 | 15.64 | 7.897 | 23 |
VarSEAK | No splicing effect | No splicing effect | New DSS | No splicing effect | No splicing effect | No splicing effect | Cryptic DSS activated |
MaxEntScan | No change | No change | New DSS | No change | No change | No change | Cryptic DSS activated |
NetGene2 | No change | No change | New DSS | No change | No change | No change | Cryptic DSS activated |
NNSplice | No change | No change | New DSS | No change | No change | No change | Cryptic DSS activated |
PhD-SNPg | Pathogenic | Benign | Pathogenic | Benign | Benign | Benign | Pathogenic |
Pmut | Neutral | Neutral | NA | Neutral | Neutral | NA | Neutral |
Frequency in 1000 Genomes Project | NA | NA | NA | 0.003 | 0.001 | 0.008 | 0.001 |
Frequency in gnomAD | NA | 0.000004 | NA | 0.003 | 0.001 | 0.008 | 0.001 |
ACMG | VUS | Likely benign | VUS | Likely benign | Likely benign | Likely benign | Likely benign |