SCN5A Variant A1100T
Summary of observed carriers, functional annotations, and structural context for SCN5A A1100T. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
3%
0/11 effective observations
Estimated BrS1 penetrance
6%
0/11 effective observations
Total carriers
1
0 BrS1 · 0 LQT3 · 1 unaffected
Variant features alone are equivalent to phenotyping 0 individuals for Brugada syndrome and 0 individuals for LQT3.
In silico predictors
| PROVEAN | PolyPhen-2 | BLAST-PSSM | REVEL | Penetrance Density BrS (%) | Penetrance Density LQT3 (%) |
|---|---|---|---|---|---|
| -0.32 | 0.009 | 1.34 | 0.311 | 3 | 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
| Source | Year | Carriers | Unaffected | LQT3 | BrS1 | Other | Other Disease |
|---|---|---|---|---|---|---|---|
| Literature, cohort, and gnomAD | – | 1 | 1 | 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.
| Neighbour residue | Distance (Å) | Observed variants |
|---|---|---|
| 1085 | 15 | |
| 1086 | 14 | |
| 1087 | 14 | |
| 1088 | 13 | A1088T, A1088V, |
| 1089 | 13 | |
| 1090 | 12 | P1090Q, P1090L, |
| 1091 | 11 | D1091Y, D1091A, |
| 1092 | 11 | |
| 1093 | 10 | |
| 1094 | 9 | |
| 1095 | 8 | W1095C, W1095X, W1095C, |
| 1096 | 8 | S1096G, S1096C, |
| 1097 | 7 | Q1097H, Q1097H, c.3288+2delT, |
| 1098 | 5 | V1098L, V1098M, V1098L, |
| 1099 | 4 | |
| 1100 | 0 | A1100T, A1100V, |
| 1101 | 4 | |
| 1102 | 5 | A1102T, |
| 1103 | 7 | S1103F, S1103Y, |
| 1104 | 8 | |
| 1105 | 8 | E1105V, E1105X, |
| 1106 | 9 | A1106T |
| 1107 | 10 | E1107X, E1107K, p.E1107RfsX24, |
| 1108 | 11 | |
| 1109 | 11 | S1109G, |
| 1110 | 12 | |
| 1111 | 13 | |
| 1112 | 13 | Q1112X, |
| 1113 | 14 | A1113V, A1113T, |
| 1114 | 14 | D1114E, D1114E, D1114N, |
| 1115 | 15 | W1115R, W1115R, W1115X, |