SCN5A Variant A1102T

Summary of observed carriers, functional annotations, and structural context for SCN5A A1102T. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

3%

0/13 effective observations

Estimated BrS1 penetrance

2%

0/13 effective observations

Total carriers

3

0 BrS1 · 0 LQT3 · 3 unaffected

A1102T is present in 3 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 0 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 (%)
0.08 0 0.73 0.229 1 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 – 3 3 0 0 –
Variant features alone – 15 15 0 0 – –

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 A1102T.
Neighbour residue Distance (Å) Observed variants
1087 15
1088 14 A1088V, A1088T,
1089 14
1090 13 P1090L, P1090Q,
1091 13 D1091A, D1091Y,
1092 12
1093 11
1094 11
1095 10 W1095C, W1095C, W1095X,
1096 9 S1096C, S1096G,
1097 8 c.3288+2delT, Q1097H, Q1097H,
1098 8 V1098M, V1098L, V1098L,
1099 7
1100 5 A1100T, A1100V,
1101 4
1102 0 A1102T,
1103 4 S1103Y, S1103F,
1104 5
1105 7 E1105V, E1105X,
1106 8 A1106T,
1107 8 p.E1107RfsX24, E1107K, E1107X,
1108 9
1109 10 S1109G,
1110 11
1111 11
1112 12 Q1112X,
1113 13 A1113T, A1113V,
1114 13 D1114E, D1114E, D1114N,
1115 14 W1115X, W1115R, W1115R,
1116 14 R1116W, R1116Q,
1117 15