SCN5A Variant S199T
Summary of observed carriers, functional annotations, and structural context for SCN5A S199T. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
1%
0/11 effective observations
Estimated BrS1 penetrance
8%
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 (%) |
|---|---|---|---|---|---|
| -0.61 | 0.951 | -0.32 | 0.578 | 7 | 0 |
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 |
|---|---|---|
| 223 | 12 | V223L, |
| 198 | 6 | |
| 193 | 11 | W193R, W193X, |
| 209 | 15 | N209T, N209S, |
| 195 | 5 | |
| 228 | 12 | K228R, |
| 227 | 12 | L227P, |
| 171 | 12 | |
| 197 | 7 | |
| 221 | 9 | |
| 196 | 6 | |
| 190 | 15 | R190L, R190Q, R190W, R190G, |
| 169 | 12 | |
| 189 | 8 | |
| 222 | 11 | R222L, R222X, R222Q, |
| 224 | 9 | L224F, |
| 191 | 12 | |
| 226 | 13 | A226V, A226G, |
| 205 | 11 | c.612-2A>G, Y205X, |
| 206 | 10 | |
| 217 | 12 | |
| 172 | 11 | |
| 185 | 12 | A185T, A185V, |
| 199 | 0 | S199T, |
| 165 | 13 | |
| 204 | 9 | c.611+1G>A, A204T, c.611+3_611+4dupAA, A204V, |
| 203 | 6 | |
| 208 | 14 | E208K, |
| 192 | 10 | |
| 168 | 11 | |
| 175 | 13 | K175N, |
| 202 | 5 | I202T, |
| 194 | 9 | |
| 141 | 15 | I141N, I141V, |
| 188 | 11 | |
| 201 | 6 | |
| 219 | 15 | R219C, R219H, c.656_657insATTCA, p.R219HfsX11, |
| 225 | 9 | R225Q, R225W, |
| 218 | 11 | |
| 176 | 14 | |
| 207 | 12 | |
| 186 | 14 | |
| 200 | 4 | |
| 187 | 14 | T187I, T187S, |
| 220 | 13 | T220I, |