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. 2014 Mar 4;99(7):635–640. doi: 10.1136/archdischild-2013-305331

Table 3 .

In silico analysis of long QT genetic variants found in eight victims of SIDS

Gene RefSeq accession numbers (transcript and protein) and UniProt number Variant position (transcript, protein and exon) Bioinformatic programmes Interpretation
PolyPhen-2a,* Mutation Assessorb (Functional Impact) I-MUTANT 3.0c PMutd MutPrede SNPs&GOf PANTHERg
KCNQ1 NM_000218.2
NP_000209.2
P51787
c.436G>A
p.E146K
E2
Benign (Scores: 0.250; 0.134) Neutral Disease (RI 6.0) Neutral (RS 0) Pdel: 0.859 Disease (RI 5.0) Pdel: 0.31 Pathogenic (LQTS1)
KCNH2 NM_000238.2
NP_000229.1
Q12809
c.3140G>T
p.R1047L
E13
Benign (Scores: 0.039; 0.020) Low Disease (RI 2.0) Pathological (RS 8) Pdel: 0.373 Disease (RI 1.0) Pdel: 0.42 Pathogenic (LQTS2)
SCN5A NM_198056.2
NP_932173.1
Q14524
c.1673A>G
p.H558R
E6
Benign (Scores: 0.000; 0.000) Neutral Neutral (RI 6.0) Neutral (RS 6) Pdel: 0.086 Neutral (RI 8.0) Pdel: 0.14 Polymorphism
c.2275A>T†
p.I759F
E15
Benign (Scores: 0.003; 0.007) Medium Disease (RI 5.0) Neutral (RS 3) Pdel: 0.878 Disease (RI 7.0) Pdel: 0.54 Pathogenic (LQTS3)
c.3578G>A
p.R1193Q
E20
Benign (Scores: 0.001; 0.006) Low‡ Disease (RI 6.0) Pathological (RS 3) Pdel: 0.825 Neutral (RI 4.0) Pdel: 0.28 Uncertain
c.4565T>A†
p.F1522Y
E27
Benign (Scores: 0.417; 0.116) Low Neutral (RI 1.0) Neutral (RS 8) Pdel: 0.823 Disease (RI 4.0) Possibly pathogenic (LQTS3)

d. http://mmb2.pcb.ub.es:8080/PMut/; RS refers to Reliability Score.

e. http://mutpred.mutdb.org/; Pdel refers to the probability that the variant is a deleterious mutation.

f. http://snps-and-go.biocomp.unibo.it/snps-and-go/; RI refers to Reliability Index.

g. http://www.pantherdb.org/tools/csnpScoreForm.jsp; Pdel refers to the probability that a given variant will cause a deleterious effect on protein function.

*Scores relate to predictions based on HumDiv and HumVar models.

†Not previously reported.

‡Accelerates the inactivation of the sodium channel current and exhibits reduced sodium channel current at the end of phase I of the action potential (taken from report provided by Mutation Assessor).

LQTS, long QT syndrome; SIDS, sudden infant death syndrome.