Skip to main content

Table 2 Pathogenicity of missense mutations within our current sample of individuals with the CDKL5 disorder

From: There is variability in the attainment of developmental milestones in the CDKL5 disorder

Nucleotide change (cDNA) Protein change SIFT (score 1–0) MutationTaster (pvalue 0–1) PolyPhen2 (score 0–1) Align GVGD (Class C0–C65)
c.38 T > C p.Phe13Ser Deleterious (0) Disease-causing (0.999) Probably damaging (0.999) Benign (C0)
c.58G > C p.Gly20Arg Deleterious (0) Disease-causing (1) Probably damaging (0.985) Benign (C0)
c.119C > T p.Ala40Val Tolerated (0.12) Disease-causing (0.999) Probably damaging (0.999) Benign (C0)
c.191 T > C p.Leu64Pro Deleterious (0) Disease-causing (1) Probably damaging (1) Benign (C0)
c.364G > A p.Ala122Thr Deleterious (0) Disease-causing (1) Probably damaging (0.999) Likely pathogenic (C55)
c.377G > A p.Cys126Tyr Deleterious (0) Disease-causing (1) Probably damaging (1) Pathogenic (C65)
c.395 T > G p.Val132Gly Deleterious (0) Disease-causing (1) Probably damaging (1) Pathogenic (C65)
c.428 T > A p. Ile143Asn Deleterious (0) Disease-causing (1) Possibly damaging (0.9) Benign (C0)
c.458A > T p. Asp153Val Deleterious (0) Disease-causing (1) Benign (0.07) Benign (C0)
c.473G > C p.Arg158Pro Deleterious (0) Disease-causing (1) Probably damaging (0.999) Benign (C0)
c.514G > A p.Val172le Deleterious (0) Disease-causing (1) Probably damaging (0.995) Benign (C0)
c.526 T > C p. Trp176Arg Deleterious (0) Disease-causing (1) Probably damaging (0.999) Benign (C0)
c.532C > T p.Arg178Trp Deleterious (0) Disease-causing (1) Probably damaging (1) Benign (C0)
c.536C > T p. Ser179Phe Deleterious (0) Disease-causing (1) Probably damaging (0.999) Likely benign (C15)
c.577G > C p.Asp193His Deleterious (0) Disease-causing (1) Probably damaging (1) Pathogenic (C65)
c.587C > T p.Ser196Leu Deleterious (0) Disease-causing (1) Probably damaging (0.976) Pathogenic (C65)
c.595 T > C p.Cys199Arg Deleterious (0) Disease-causing (1) Probably damaging (0.999) Pathogenic (C65)
c.620G > A p.Gly207Glu Deleterious (0) Disease-causing (1) Probably damaging (1) Pathogenic (C65)
c.656A > C p.Gln219Pro Deleterious (0) Disease-causing (1) Probably damaging (0.996) Pathogenic (C65)
c.680 T > C p.Leu227Pro Deleterious (0) Disease-causing (1) Probably damaging (0.996) Pathogenic (C65)
c.2684C > T p.Pro895Leu Deleterious (0.03) Disease causing (1) Possibly damaging (0.578) Benign (C0)
c.872G > A p.Cys291Tyr Deleterious (0.01) Disease causing (1) Probably damaging (0.930) Benign (C0)
c.215 T > C p.Ile72Thr Deleterious (0) Disease-causing (1) Possibly damaging (0.578) Benign (C0)
c.1612A > G p.Thr538Ala Deleterious (0.04) Polymorphism (1) Benign (0.009) Benign (C0)
c.526 T > C p.Trp167Arg Deleterious (0) Disease causing (1) Probably damaging (0.999) Benign (C0)
  1. CDKL5 numbering based on GenBank reference sequences NG_008475.1 and NM_003159.2, with the first A in the start codon numbered +1. In silico predictions are carried out through Alamut Visual (v2.4) using SIFT (scale: 1 = tolerated, 0 = deleterious) [26], MutationTaster (p value for prediction confidence (not pathogenicity): 0 = low confidence, 1 = high confidence) [27], PolyPhen2 (HumVar module, scale: 0 = benign, 1 = probably damaging) [28], Align GVGD (scale: C0 = benign, C65 = pathogenic) [29].