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Table 4 Rare or novel mutations identified in candidate genes by association studies

From: Identification of sequence variants associated with severe microtia-astresia by targeted sequencing

Sample ID Gene Symbol Consequence GenBank accession No. Exon Mutation PopFreqMax in 1000GM, ESP6500 or gnomAD SIFT_score SIFT_Pred Polyphen2_HDIV_score Polyphen2_HDIV_pred Phylop in vertebrate HGMD
XH1790 DCHS1 nonsynonymous NM_003737 exon2 c. 481C > T, p.R161C 0.00003335 0.069 T 1 D −0.001 NR
XH1785 FREM2 nonsynonymous NM_207361 exon22 c. 8689C > T, p.R2897C . 0 D 1 D 0.871 NR
1552 *GBA nonsynonymous NM_001005741 Exon10 c. 1292A > G, p.N431S 0.00001657 0.169 T 0.962 D 0.991 DM?
1454 PLEC nonsynonymous NM_201378 exon31 c.5273C > T, p.A1758V 0.0001578 0.535 T 1 D 0.897 NR
1467 PLEC nonsynonymous NM_201378 exon32 c.11563G > A, p.G3855S 0.00002367 0.652 T 0 B −2.741 NR
  USH2A nonsynonymous NM_007123 exon6 c.1007A > G, p.N336S . 0.048 D 0.218 B 0.991 NR
XH1582 PLEC nonsynonymous NM_000445 exon2 c. 115A > G, p.S39G 0.001536 0.381 T 0.002 B 0.991 NR
XH1535 POMT1 nonsynonymous NM_001136114 exon16 c. 1428G > C, p.L476F 0.0001156 0.556 T 0.001 B −0.043 NR
XH1546 POMT1 nonsynonymous NM_001136114 exon16 c. 1428G > C, p.L476F 0.0001156 0.556 T 0.001 B −0.043 NR
  USH2A nonsynonymous NM_206933 exon42 c. 8420C > T, p.T2807I . 0.065 T 0.998 D 0.917 NR
XH1563 GLI3 nonframeshift NM_000168 exon15 c. 3107C > T, p.A1036V 0.00007006 0.016 D 0 B 0.897 NR
XH1594 GLI3 nonsynonymous NM_000168 exon7 c. 857C > T, p.A286V . 0.18 T 0.024 B 0.917 NR
  *USH2A nonsynonymous NM_206933 exon63 c.12344G > A, p.R4115H 0.0005825 0.072 T 0.462 P 0.871 DM
1575 USH2A nonsynonymous NM_206933 exon27 c. 5389A > G, p.N1797D . 1 T 0 B −0.068 NR
1742 USH2A nonsynonymous NM_206933 exon57 c.11123C > T, p.P3708L . 0.223 T 1 D 0.917 NR
XH1566 USH2A nonsynonymous NM_206933 exon55 c.10871A > G, p.Q3624R . 0.271 T 0.012 B 0.079 NR
XH1579 *USH2A nonsynonymous NM_206933 exon63 c.13157 T > C, p.I4386T . 0.006 D 0.978 D 1.062 DM
  USH2A nonsynonymous NM_206933 exon56 c.10958A > G, p.N3653S . 0.409 T 0.489 P 0.991 NR
  USH2A nonsynonymous NM_007123 exon6 c. 1105G > A, p.V369 M . 0.015 D 0.992 D 0.871 NR
  1. Notes: *indicates the mutation has been reported in HGMD database
  2. Abbreviations: SIFT: D Deleterious, T Tolerated; PolyPhen 2: D = Probably damaging, B Benign, P Possibly damaging; NR not reported, DM: “disease causing” mutation