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Table 1 List of variants found in cohort classified as Pathogenic or Likely Pathogenic

From: Detection rate of causal variants in severe childhood epilepsy is highest in patients with seizure onset within the first four weeks of life

Gene

Ref Seq

DNA-level

Protein level

AD/AR

DN/INH

Prediction (SIFT, PolyPhen2,ClinVar)

ExAC all

Pathogenic AD variants

 CACNA1A

NM_001127221.1

c.13319826G > T

 

AD

DN

    

 CACNA1A

NM_001127221.1

c.2663A > T

p.Gln888Leu

AD

DN

   

0.0005

 dup chr9

CNV

AD

DN

    

 GABRB3

NM_000814.5

c.841A > G

p.Thr281Ala

AD

DN

D

PD

  

 GABRG2

NM_000816.3

c.968G > A

p.Arg323Gln

AD

DN

D

PD

  

 GRIN1

NM_007327.3

c.2443G > A

p.Gly815Arg

AD

DN

D

PD

P

 

 GRIN1

NM_007327.3

c.1643G > A

p.Arg548Gln

AD

DN

T

PD

  

 HCN1

NM_021072.3

c.1189A > G

p.Ile397Leu

AD

DN

T

B

  

 KCNQ2

NM_172107.2

c.826A > C

p.Thr276Pro

AD

DN

D

B

  

 KCNQ2

NM_172107.2

c.1004C > G

p.Pro335Arg

AD

DN

D

PD

  

 KCNQ2

NM_172107.2

c.701C > T

p.Thr234Ile

AD

DN

D

PD

  

 KCNQ2

NM_172107.2

c.913_915delTTC

p.Phe305del

AD

DN

    

 KCNQ2

NM_172107.2

c.913_915delTTC

p.Phe305del

AD

DN

    

 MEF2C

NM_002397.4

c.766C > T

p.Arg256*

AD

DN

    

 PURA

NM_005859.4

c.812_814del

p.Phe271del

AD

DN

    

 SCN1A

NM_001202435.1

c.1244 T > A

p.Ile415Lys

AD

DN

D

PD

  

 SCN1A

NM_001165963.1

c.5384A > G

p.Glu1795Gly

AD

DN

D

PD

  

 SCN1A

NM_001165963.1

c.4384dup

p.Tyr1462Leufs*24

AD

DN

    

 SCN1A

NM_001165963.1

c.1178G > A

p.Arg393His

AD

DN

D

PD

P

 

 SCN1A

NM_001165963.1

c.1525C > T

p.Gln509*

AD

DN

    

 SCN2A

NM_001040142.1

c.2774 T > C

p.Met925Thr

AD

DN

D

PD

  

 SCN2A

NM_001040142.1

c.5009C > T

p.Thr1862Ile

AD

DN

T

PD

  

 SCN8A

NM_014191.3

c.4921C > G

p.Leu1641Val

AD

DN

D

PD

  

 SCN8A

NM_014191.3

c.2549G > A

p.Arg850Gln

AD

DN

D

PD

LP

 

 SCN8A

NM_014191.3

c.4850G > T

p.Arg1617Leu

AD

DN

D

PD

  

 STXBP1

NM_003165.3

c.1654 T > C

p.Cys552Arg

AD

DN

D

B

  

 UBE3A

NM_130838.1

c.1149G > C

p.Glu383Asp

AD

INH

    

Pathogenic AR variants

 ALDH7A1

NM_001182.4

c.1318-1G > C

 

AR

INH

   

0.00041

 ALDH7A1

NM_001182.4

c.518-14_518delinsCA

 

AR

INH

    

 SLC13A5

NM_177550.3

c.425C > T

p.Thr142Met

AR

INH

D

PD

P

0.00081

 TREX1

NM_016381.3

c.10621072del

p.Leu354Phefs*22

AR

UNK

    

 TREX1

NM_016381.3

c.1072A > C

p.Thr358Pro

AR

INH

T

 

P

0.0016

Pathogenic X-linked variants

 CDKL5

NM_003159.2

c.2578C > T

p.Gln860*

XL

DN

    

 CDKL5

NM_003159.2

c.463 + 5G > A

 

XL

DN

    

 CDKL5

NM_003159.2

c.1247_1248del

p.Glu416Valfs*2

XL

DN

  

P

 

 IQSEC2

NM 001111125.2

c.3206G > C

p.Arg1069Pro

XL

INH

D

PD

  

 MECP2

NM_004992.3

c.1219_1229del

p.Asp407Glnfs*25

XL

DN

    

 WDR45

NM_007075.3

c.654del

p.Arg219Alafs*69

XL

DN

    

 WDR45

NM_007075.3

c.970_971del

p.Val324Hisfs*17

XL

DN

    

 WDR45

NM_007075.3

c.511C > T

p.Gln171*

XL

DN

    

 WDR45

NM_007075.3

c.344 + 4A > C

 

XL

DN

    

Likely pathogenic variants

 CHD2

NM_001271.3

c.3782G > A

p.Trp1261*

AD

UNK

    

 MECP2

NM_004992.3

c.925C > T

p.Arg309Trp

XL

INH

D

PD

VUS

 

 PCDH19

NM_001184880.1

c.698A > G

p.Asp233Gly

XL

INH

D

PD

  
  1. Legend: Data were analysed by SureCall and NextGENe with parameters mentioned in the methods section
  2. SIFT – D: deleterious, T: tolerated;
  3. PolyPhen2 PD probably damaging, B benign, PoD possible damaging;
  4. ClinVar – VUS Variant of uncertain significance, P pathogenic;
  5. AR autosomal recessive, AD autosomal dominant, XL X-linked, INH inherited, DN de novo
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Orphanet Journal of Rare Diseases

ISSN: 1750-1172