SCN5A Variant L342R
Summary of observed carriers, functional annotations, and structural context for SCN5A L342R. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
31%
1/10 effective observations
Estimated BrS1 penetrance
15%
1/10 effective observations
Total carriers
0
0 BrS1 · 0 LQT3 · 0 unaffected
Variant features alone are equivalent to phenotyping 1 individuals for Brugada syndrome and 1 individuals for LQT3.
In silico predictors
| PROVEAN | PolyPhen-2 | BLAST-PSSM | REVEL | Penetrance Density BrS (%) | Penetrance Density LQT3 (%) |
|---|---|---|---|---|---|
| NA | NA | NA | 0.859 | 14 | 40 |
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 | – | 0 | 0 | 0 | 0 | – | |
| Variant features alone | – | 15 | 13 | 1 | 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.
| Neighbour residue | Distance (Å) | Observed variants |
|---|---|---|
| 328 | 10 | |
| 333 | 15 | c.998+1G>A, c.998+5G>A, |
| 277 | 9 | |
| 326 | 9 | |
| 276 | 12 | L276Q, L276P, |
| 348 | 14 | P348A, |
| 317 | 11 | K317E, K317M, K317N, K317N, |
| 279 | 6 | |
| 385 | 14 | A385T, |
| 338 | 12 | |
| 278 | 6 | H278D, H278R, |
| 334 | 13 | c.999-424_1338+81del, |
| 318 | 14 | |
| 332 | 15 | A332T, |
| 343 | 6 | |
| 327 | 9 | |
| 339 | 10 | |
| 384 | 11 | S384T, |
| 284 | 14 | |
| 329 | 14 | |
| 282 | 11 | R282C, R282H, |
| 340 | 6 | R340W, R340Q, |
| 283 | 10 | |
| 1550 | 13 | |
| 341 | 4 | C341Y, |
| 274 | 11 | G274C, |
| 273 | 15 | |
| 335 | 11 | C335S, C335R, C335S, |
| 319 | 12 | G319S, G319R, G319C, |
| 325 | 10 | L325R, |
| 324 | 13 | |
| 321 | 12 | S321Y, |
| 345 | 9 | |
| 275 | 11 | N275K, N275K, |
| 383 | 14 | |
| 280 | 7 | C280Y, |
| 323 | 11 | |
| 347 | 13 | |
| 320 | 10 | T320N, |
| 342 | 0 | |
| 1551 | 14 | D1551N, D1551Y |
| 346 | 13 | E346K, E346G, E346X, E346D, E346D, |
| 336 | 12 | P336L, |
| 344 | 6 | A344S, |
| 322 | 14 | |
| 281 | 5 | V281M, |