SCN5A Variant S1096G

Summary of observed carriers, functional annotations, and structural context for SCN5A S1096G. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

2%

0/11 effective observations

Estimated BrS1 penetrance

10%

1/11 effective observations

Total carriers

1

0 BrS1 · 0 LQT3 · 1 unaffected

S1096G is present in 1 alleles in gnomAD. This residue resides in a Non_Hotspot region for Brugada syndrome and a Non_Hotspot region for LQT3.

Variant features alone are equivalent to phenotyping 1 individuals for Brugada syndrome and 0 individuals for LQT3.

In silico predictors

Variant-level computational predictors.
PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density BrS (%) Penetrance Density LQT3 (%)
-0.44 0.963 -1.15 0.587 8 2

PROVEAN scores below -2 suggest deleterious impact. REVEL scores above 0.5–0.75 are often interpreted as likely pathogenic. PolyPhen-2 scores above 0.85 are typically pathogenic. Penetrance density summarises neighbouring residue risk (Kroncke et al. 2019).

Reported carrier data

Observed carriers by publication or cohort.
Source Year Carriers Unaffected LQT3 BrS1 Other Other Disease
Literature, cohort, and gnomAD – 1 1 0 0 –
Variant features alone – 15 14 0 1 – –

Totals may differ from individual publications due to duplicate patients removed during curation.

Nearby variants

Neighbouring residues within 15 Ångström provide structural context. Variants listed in the right-most column have been observed clinically or in gnomAD.

Previously observed variants near S1096G.
Neighbour residue Distance (Å) Observed variants
1081 15
1082 14 V1082A,
1083 14 S1083C,
1084 13 G1084S, G1084R, G1084D,
1085 13
1086 12
1087 11
1088 11 A1088T, A1088V,
1089 10
1090 9 P1090Q, P1090L,
1091 8 D1091A, D1091Y,
1092 8
1093 7
1094 5
1095 4 W1095X, W1095C, W1095C,
1096 0 S1096C, S1096G,
1097 4 Q1097H, c.3288+2delT, Q1097H,
1098 5 V1098L, V1098L, V1098M,
1099 7
1100 8 A1100T, A1100V,
1101 8
1102 9 A1102T,
1103 10 S1103F, S1103Y,
1104 11
1105 11 E1105V, E1105X,
1106 12 A1106T,
1107 13 p.E1107RfsX24, E1107X, E1107K,
1108 13
1109 14 S1109G,
1110 14
1111 15