Table 1 USH2A variants in the current study and its pathogenicity prediction analysis.
From: Allelic hierarchy for USH2A influences auditory and visual phenotypes in South Korean patients
Genomic position (GRCh37/hg19) | HGVS | Location (Exon/domain) | In-silico Prediction | Allele Frequency | Clinvar database | ACMG/AMP 2018 guideline | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|
Nucleotide change | Amino Acid change | CADD | REVEL | Splice AI Maxent | KOVA KRGDB | gnomAD | Classificatioin | Criteria | Classification | ||
Chr1:216595428C-T | c.251G > A | p.Cys84Tyr | Exon 2/Absent | 22.90 | 0.483 | NA | ND | ND | Uncertain significance | PM2, PM3, PP4 | Uncertain significance |
Chr1:216420527G-A | c.2209C > T | p.Arg737* | Exon 13/Laminin EGF like 4 | 36.00 | NA | NA | ND | exome (8.151e−06) genome(ND) | Pathogenic (PMID10729113) | ||
Chr1:216419934A-C | c.2802 T > G | p.Cys934Trp | Exon 13/Laminin EGF like 8 | 25.20 | 0.849 | NA | 0.00291206 | exome(0.0002111)gnome(0.0001274) | Conflicting Pathogenic(10); Likely pathogenic(3); Uncertain significance(3) | PS1, PM3, PP3, PP4 | Likely pathogenic |
Chr1:216270451G-A | c.4732C > T | p.Arg1578Cys | Exon 22/Laminin G-like 1 | 24.20 | 0.695 | NA | ND | exome(1.593e−05) genomes(3.185e−05) | Pathogenic (PMID22135276) | ||
Chr1:216262383G-A | c.4858C > T | p.Gln1620* | Exon 23/Laminin G like 1 | 37.00 | NA | NA | ND | ND | Likely pathogenic (PMID21697857) | ||
Chr1:215963842 T-C | c.7120 + 1475A > G | p.? | Intron 37 | 22.40 | NA | DG(0.25) DL(0.00) MAXENT (NA) | ND | ND | ND | PVS1, PM2, PM3 | Pathogenic |
Chr1:216052432C-G | c.8232G > C | p.Trp2744Cys | Exon 42/Fibronectin type III 14 | 29.30 | 0.651 | NA | ND | exome(8.296e−06) genome(ND) | Pathogenic (PMID21686329) | ||
Chr1:216051224 T-C | c.8559-2A > G | p.? | Intron 42 | 34.00 | NA | AG(0.00) AL(0.99) /MAXENT (2.13) | ND | exome(3.186e−05) genome(ND) | Pathogenic (PMID10729113) | ||
Chr1:215955530A-T | c.10593del | P.Ile3532Phefs*18 | Exon 54/Fibronectin type III 20 | ND | NA | NA | ND | ND | ND | PVS1, PM2, PM3 | Pathogenic |
Chr1:215955412G-A | c.10712C > T | p.Thr3571Met | Exon 54/Fibronectin type III 20 | 25.30 | 0.622 | NA | ND | exome(1.194e−05) gemone(ND) | Pathogenic (PMID19683999) | ||
Chr1:215955400C-A | c.10724G > T | p.Cys3575Phe | Exon 54/Fibronectin type III 20 | 28.00 | 0.367 | NA | ND | ND | ND | PM2, PM3, PM5, PP4 | Likely pathogenic |
Chr1:215933077C-T | c.11156G > A | p.Arg3719His | Exon 57/Fibronectin type III 22 | 25.80 | 0.334 | NA | 0.00029121 | exome(5.283E−05) genome(9.689E−05) | Pathogenic (PMID25133613) | ||
Chr1:215848545A-T | c.12708 T > A | p.Cys4236* | Exon 63/Fibronectin type III 27 | 41.00 | NA | NA | ND | ND | Pathogenic (PMID21593743) | ||
Chr1:215848137CATT-C | c.13112_13115del | p.Gln4371Argfs*19 | Exon 63/Fibronectin type III 29 | 33.00 | NA | NA | ND | exome(1.221e−05) genome(3.184e−05) | Pathogenic/Likely pathogenic (PMID28894305) | ||
Chr1:215844483A-G | c.13964 T > C | p.Leu4655Pro | Exon 64/Fibronectin type III 32 | 27.80 | 0.529 | NA | ND | ND | ND | PM2, PM3, PP4 | Uncertain Significance |
Chr1:215827321 T-C | c.14134-3169A > G | p.? | Intron 64 | 3.30 | NA | AG(0.02) AL(0.00) MAXTENT (NA) | ND | ND | Pathogenic (PMID29196752) | ||
Chr1:215814032CA-A | c.14835del | p.Val4946Trpfs*4 | Exon 68/Absent | ND | NA | NA | ND | ND | Pathogenic (PMID21697857) | ||
Chr1:215813957G-A | c.14911C > T | p.Arg4971* | Exon 68/Absent | 48.00 | NA | NA | ND | exome(ND) genome(ND) | Pathogenic (PMID10729113) | ||
