SCN5A Variant S1503Y
Summary of observed carriers, functional annotations, and structural context for SCN5A S1503Y. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
24%
1/11 effective observations
Estimated BrS1 penetrance
12%
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 1 individuals for LQT3.
In silico predictors
| PROVEAN | PolyPhen-2 | BLAST-PSSM | REVEL | Penetrance Density BrS (%) | Penetrance Density LQT3 (%) |
|---|---|---|---|---|---|
| -5.41 | 0.783 | 0.37 | 0.921 | 10 | 34 |
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 | 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 |
|---|---|---|
| 1850 | 11 | C1850S, C1850S, |
| 1855 | 13 | |
| 1794 | 12 | |
| 1849 | 13 | H1849R, |
| 1853 | 14 | I1853V |
| 1795 | 10 | Y1795N, Y1795H, p.Y1795_E1796insD, Y1795C, |
| 1652 | 15 | M1652T, M1652R, |
| 1504 | 4 | K1504E, |
| 1851 | 9 | M1851V, M1851I, M1851I, M1851I, |
| 1501 | 7 | p.L1501_K1505del, L1501V, |
| 1507 | 13 | p.Q1507_P1509del, |
| 1505 | 7 | p.K1505_Q1507del, K1505N, K1505N, |
| 1858 | 13 | |
| 1787 | 13 | S1787N, |
| 1786 | 13 | c.5356_5357delCT, L1786Q, L1786R, |
| 1648 | 15 | |
| 1807 | 13 | c.5420dupA, |
| 1495 | 12 | Y1495S, |
| 1798 | 14 | W1798X, |
| 1496 | 11 | |
| 1854 | 10 | |
| 1481 | 15 | G1481R, G1481R, G1481E, G1481V, |
| 1781 | 15 | E1781G, E1781D, E1781D, |
| 1789 | 14 | |
| 1499 | 6 | |
| 1498 | 10 | M1498V, M1498T, M1498R, |
| 1788 | 10 | c.5361_5364delTGAG, |
| 1500 | 6 | p.K1500del, |
| 1791 | 9 | |
| 1852 | 14 | D1852V, |
| 1792 | 11 | D1792N, D1792Y, D1792V, |
| 1502 | 4 | G1502S, G1502A, |
| 1497 | 9 | |
| 1790 | 14 | D1790N, D1790G, p.D1790del, |
| 1494 | 14 | |
| 1506 | 10 | P1506T, P1506S, |
| 1503 | 0 | S1503Y, |