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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].