SCN5A Variant R517S
Summary of observed carriers, functional annotations, and structural context for SCN5A R517S. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
2%
0/11 effective observations
Estimated BrS1 penetrance
16%
1/11 effective observations
Total carriers
1
0 BrS1 · 0 LQT3 · 1 unaffected
Variant features alone are equivalent to phenotyping 1 individuals for Brugada syndrome and 0 individuals for LQT3.
In silico predictors
| PROVEAN | PolyPhen-2 | BLAST-PSSM | REVEL | Penetrance Density BrS (%) | Penetrance Density LQT3 (%) |
|---|---|---|---|---|---|
| NA | 0.309 | 0.32 | 0.507 | 17 | 1 |
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 | 14 | 0 | 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 |
|---|---|---|
| 502 | 15 | |
| 503 | 14 | P503S, |
| 504 | 14 | R504T, |
| 505 | 13 | A505E, |
| 506 | 13 | M506K, |
| 507 | 12 | p.N507_L515dup, |
| 508 | 11 | |
| 509 | 11 | |
| 510 | 10 | |
| 511 | 9 | |
| 512 | 8 | T512I, |
| 513 | 8 | R513P, c.1537delC, R513H, R513C, |
| 514 | 7 | G514C, |
| 515 | 5 | |
| 516 | 4 | |
| 517 | 0 | R517S, R517S, |
| 518 | 4 | |
| 519 | 5 | S519F, |
| 520 | 7 | M520R, M520V, |
| 521 | 8 | K521E, c.1562delA, |
| 522 | 8 | P522S, |
| 523 | 9 | R523C, R523S, R523H, |
| 524 | 10 | S524Y, c.1570_1571insG, |
| 525 | 11 | S525G, |
| 526 | 11 | R526H, R526C, |
| 527 | 12 | G527R, G527R, |
| 528 | 13 | S528R, S528R, S528R, |
| 529 | 13 | |
| 530 | 14 | F530V, F530S, |
| 531 | 14 | T531A, T531I, |
| 532 | 15 | F532L, F532C, F532L, F532L, |