SCN5A Variant S1079T

Summary of observed carriers, functional annotations, and structural context for SCN5A S1079T. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

1%

0/16 effective observations

Estimated BrS1 penetrance

13%

2/16 effective observations

Total carriers

6

0 BrS1 · 0 LQT3 · 6 unaffected

S1079T is present in 6 alleles in gnomAD. This residue resides in a Hotspot region for Brugada syndrome and a Non_Hotspot region for LQT3.

Variant features alone are equivalent to phenotyping 2 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 (%)
-0.43 0.071 -0.06 0.391 33 3

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 – 6 6 0 0 –
Variant features alone – 15 13 0 2 – –

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 S1079T.
Neighbour residue Distance (Å) Observed variants
1064 15 p.E1064del,
1065 14
1066 14 S1066G,
1067 13 L1067R,
1068 13 G1068A, G1068D,
1069 12 T1069M,
1070 11
1071 11 E1071K, p.E1071GfsX76,
1072 10 p.E1072del,
1073 9
1074 8 S1074R, S1074R, S1074R, S1074G,
1075 8
1076 7
1077 5 c.3228+2delT,
1078 4
1079 0 S1079F, S1079T, S1079Y,
1080 4
1081 5
1082 7 V1082A,
1083 8 S1083C,
1084 8 G1084S, G1084R, G1084D,
1085 9
1086 10
1087 11
1088 11 A1088T, A1088V,
1089 12
1090 13 P1090Q, P1090L,
1091 13 D1091A, D1091Y,
1092 14
1093 14
1094 15