SCN5A Variant R533S
Summary of observed carriers, functional annotations, and structural context for SCN5A R533S. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
4%
0/15 effective observations
Estimated BrS1 penetrance
6%
0/15 effective observations
Total carriers
5
0 BrS1 · 0 LQT3 · 5 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 (%) |
---|---|---|---|---|---|
-4.36 | 0.997 | -2.07 | 0.708 | 2 | 7 |
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 | – | 5 | 5 | 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 |
---|---|---|
518 | 15 | |
519 | 14 | S519F, |
520 | 14 | M520V, M520R, |
521 | 13 | K521E, c.1562delA, |
522 | 13 | P522S, |
523 | 12 | R523H, R523C, R523S, |
524 | 11 | c.1570_1571insG, S524Y, |
525 | 11 | S525G, |
526 | 10 | R526C, R526H, |
527 | 9 | G527R, G527R, |
528 | 8 | S528R, S528R, S528R, |
529 | 8 | |
530 | 7 | F530S, F530V, |
531 | 5 | T531A, T531I, |
532 | 4 | F532L, F532L, F532L, F532C, |
533 | 0 | R533H, R533S, R533C, |
534 | 4 | |
535 | 5 | R535Q, R535G, R535X, |
536 | 7 | D536H, |
537 | 8 | |
538 | 8 | G538D, |
539 | 9 | |
540 | 10 | |
541 | 11 | |
542 | 11 | |
543 | 12 | F543L, F543L, F543L |
544 | 13 | |
545 | 13 | |
546 | 14 | |
547 | 14 | |
548 | 15 |