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. 2014 Sep 25;4:6470. doi: 10.1038/srep06470

Table 1. SCN1B variants identified in this study.

Nomenclature     Frequencies Nucleotide conservation Prediction of pathogenicity of missense change Predicted effect on splicing
    A       ESP (NCBI GO)4 mm;mM;MM (tot)                        
Variant 1 Isoform 2 B Patient3 dbSNP Allelic count and frequency in this study (145 patients) [avr. read depth] MAF 1000 Genomes PhyloP Pfam SIFT Polyphen2 (HumDiv/HumVar) SNAP SNPs3D Panther MutPred NetGene SpliceView NNSplice
g.35521779G>T c.40+15G>T   rs72556351:G>T G = 232/T = 58 0/616 0.169 0.008 0.448             Nsc Nc Nc
  c.40+15G>T     G = 0.8/T = 0.2 [1]                   Nsc Nc Nc
g.35523435C>A c.44C>A (p.Ser15Tyr) # 1 - C = 289/A = 1 0/6503 n.r.- 0.992 2.142 Tol Dam/Ben Neu Ben Not del Not del Nsc Cryptic acceptor lost Nsc
  c.44C>A (p.Ser15Tyr)     C = 0.997/A = 0.003 [77]       Tol Dam/Dam Not Neu Ben   Not del Nsc Cryptic acceptor lost Nsc
g.35524783G>A c.448+140G>A # 2 - G = 289/A = 1 0/3597 n.r. 0 −0.44             Nsc Nc Nc
  c.588G>A (p.Gly196Gly)     G = 0.997/A = 0.003 [21]                   Nsc Nc Nc
g.35524824T>C c.448+181T>C   rs55742440:T>C T = 162/C = 128 660;1645;1213 (3518) 0.380 0 −0.602             Nsc Nc New acceptor site
  c.629T>C (p.Leu210Pro)     T = 0.559/C = 0.441 [30]       Not tol Ben/Ben Not Neu     Not del Nsc Nc New acceptor site
g.35524836G>A c.448+193G>A # 3 rs66876876:G>A G = 289/A = 1 0;23;3455 (3478) 0.001 0 0.205             New acceptor site New acceptor site Nc
  c.641G>A (p.Arg214Gln)     G = 0.997/A = 0.003 [35]       Tol Ben/Ben Not Neu     Not del New acceptor site New acceptor site Nc
g.35524939C>A c.448+296C>A   rs67701503:C>A C = 227/A = 63 51;728;2546 (3325) 0.133 0.102 1.174             Nc Cryptic acceptor lost Nc
  c.744C>A (p.Ser248Arg)     C = 0.783/A = 0.217 [95]       Not tol Ben/Ben Not Neu     Not del Nc Cryptic acceptor lost Nc
g.35524944G>C c.448+301G>C   rs67486287:G>C G = 228/C = 62 47;681;2600 (3328) 0.129 0 0.448             Nc Cryptic acceptor lost Nc
  c.749G>C (p.Arg250Thr)     G = 0.786/C = 0.214 [99]       Not tol Ben/Ben Not Neu     Not del Nc Cryptic acceptor lost Nc
g.35530073T>C c.501T>C (p.Ile167Ile)   rs16969930:T>C T = 280/C = 10 3;302;6198 (6503) 0.014 1 0.205             New acceptor site Nc Nc
  c.*5071T>C     T = 0.966/C = 0.034 [179]                   New acceptor site Nc Nc
g.35530162C>A c.590C>A (p.Ala197Asp) # 4 - C = 289/A = 1 0/6503 n.r. 1 1.416 Not tol Dam/Ben Not Neu Dam Del Not del New donor site Nsc Nsc
  c.*5160C>A     C = 0.997/A = 0.003 [95]                        
g.35530514T>G c.591-25T>G   rs28365107:T>G T = 286/G = 4 0;143;6360 (6503) 0.006 0 −0.198             Nsc New donor site Nsc
  c.*5512T>G     T = 0.986/G = 0.014 [78]                        
g.35530525C>A c.591-14C>A   rs28365109:C>A C = 286/A = 4 0;144;6359 (6503) 0.006 0 0.044             Nsc Nsc Nsc
  c.*5523C>A     C = 0.986/A = 0.014 [86]                        
g.35530580G>A c.632G>A (p.Cys211Tyr) # 5 rs150721582:G>A G = 289/A = 1 0;4;6499 (6503) 0.001 0.992 2.869 Not tol Dam/Dam Not Neu Dam Del Not del New donor site nc Nc
  c.*5578G>A     G = 0.997/A = 0.003 [79]                        
g.35530641G>A c.*5+31G>A   rs28365108:G>A G = 288/A = 2 1;36;6466 (6503) 0.001 0 −0.198             Nsc nc Nc
  c.*5639G>A     G = 0.993/A = 0.007 [41]                        
g.35530690C>G c.*6-11C>G   rs28365105:C>G C = 266/G = 24 no coverage 0.037 0 −0.037             Nsc Nsc Nsc
  c.*5688C>G     C = 0.917/G = 0.083                          
g.35530737T>C c.*42T>C   rs2278995:T>C T = 226/C = 64 no coverage 0.148 0 −1.005             Nsc nc Nc
  c.*5735T>C     T = 0.779/C = 0.221                          
g.35530771G>T c.*76G>T # 6 - G = 289/T = 1 no coverage n.r. 0.016 0.205             Nsc nc Nc
  c.*5769G>T     G = 0.997/T = 0.003                          
g.35530781A>C c.*86A>C   rs2278996:A>C A = 224/C = 66 no coverage 0.146 0 −0.198             Nc Nsc Nc
  c.*5779A>C     A = 0.772/C = 0.228                          
g.35530797A>T c.*102A>T   rs72550274:A>T A = 288/T = 2 no coverage 0.004 0 −1.57             Nc Nsc Nc
  c.*5795A>T     A = 0.993/T = 0.007                          
g.35531222T>C c.*527T>C   rs41275828:T>C A = 277/C = 13 no coverage 0.021 0.772 0.205             Nc Nc Nc
  c.*6220T>C     A = 0.955/C = 0.045                          
g.35531229C>T c.*534C>T   rs72550266:C>T C = 289/T = 1 no coverage n.r. 0 −0.924             Nc Nc Nc
  c.*6227C>T     A = 0.997/T = 0.003                          

1Variants are listed according to their genomic position.

2Each variant is described as the expected change on transcript A [NM_001037, NP_001028] (above the line) and transcript B [NM_199037, NP_950238] (under the line) and, when present, the corresponding isoforms.

3Specific patients are referred to only for putatively pathogenic variants. As discussed in the text, pathogenicity predictions are indicated according to the output of each bioinformatic tool: Ben: Benign, Dam: damaging, Del: deleterious, Nc: no changes, Neu: neutral, Not del: not deleterious, Not neu: not neutral, Not tol: Not tolerated, n.r.: not reported, Nsc: no substantial changes, Tol: tolerated.

4Data from the NHLBI GO Exome Sequencing Project (ESP) are reported as: observed genotypes i.e., homozygosis for minor (mm) or Major (MM) allele, and heterozygosis (mM). tot: number of samples sequenced for each position. avr. read depth: the average sample read depth.