SCN5A Variant p.K1493del
Summary of observed carriers, functional annotations, and structural context for SCN5A p.K1493del. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
16%
1/13 effective observations
Estimated BrS1 penetrance
36%
4/13 effective observations
Total carriers
3
2 BrS1 · 0 LQT3 · 1 unaffected
Variant features alone are equivalent to phenotyping 2 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 | None | 26 | 33 |
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 |
|---|---|---|---|---|---|---|---|
| 23840796 | 2013 | 11 | 0 | 0 | 10 | CCD | |
| 19029124 | 2009 | 1 | 0 | 1 | 0 | ||
| 19808440 | 2009 | 1 | 0 | 1 | 0 | ||
| 20129283 | 2010 | 1 | 0 | 1 | 0 | ||
| 20129283 | 2010 | 1 | 0 | 1 | 0 | ||
| Literature, cohort, and gnomAD | – | 3 | 1 | 0 | 2 | – | |
| Variant features alone | – | 15 | 12 | 1 | 2 | – | – |
Totals may differ from individual publications due to duplicate patients removed during curation.
Functional data
Peak and late/persistent current values are relative to wild-type (100% indicates no change). V1/2 activation and inactivation denote the membrane potentials (mV) at which half-maximal current is achieved.
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 |
|---|---|---|
| 1785 | 6 | |
| 1778 | 9 | |
| 1773 | 14 | |
| 1486 | 11 | F1486L, p.F1486del, F1486L, F1486L, |
| 1652 | 15 | M1652T, M1652R, |
| 1866 | 13 | |
| 1824 | 15 | P1824A, |
| 1777 | 8 | V1777M, V1777L, V1777L, |
| 1485 | 15 | |
| 1487 | 12 | M1487L, M1487L, M1487K, |
| 1492 | 6 | |
| 1477 | 14 | K1477N, K1477N, |
| 1491 | 7 | Q1491H, Q1491H, |
| 1863 | 14 | |
| 1501 | 14 | p.L1501_K1505del, L1501V, |
| 1874 | 15 | |
| 1862 | 10 | |
| 1779 | 10 | T1779M, |
| 1493 | 0 | p.K1493del, K1493X, K1493R, |
| 1858 | 13 | |
| 1865 | 12 | |
| 1478 | 13 | K1478E, |
| 1776 | 11 | |
| 1787 | 11 | S1787N, |
| 1786 | 9 | c.5356_5357delCT, L1786Q, L1786R, |
| 1861 | 13 | V1861I, V1861F |
| 1495 | 9 | Y1495S, |
| 1774 | 14 | N1774D, c.5321_5324dupACTT, |
| 1496 | 7 | |
| 1474 | 14 | |
| 1481 | 13 | G1481R, G1481R, G1481E, G1481V, |
| 1781 | 6 | E1781G, E1781D, E1781D, |
| 1499 | 12 | |
| 1488 | 8 | T1488R, |
| 1784 | 6 | E1784K, E1784X, |
| 1498 | 11 | M1498V, M1498T, M1498R, |
| 1780 | 7 | E1780G, |
| 1788 | 14 | c.5361_5364delTGAG, |
| 1500 | 11 | p.K1500del, |
| 1859 | 14 | |
| 1869 | 15 | |
| 1791 | 14 | |
| 1482 | 12 | |
| 1868 | 12 | |
| 1783 | 8 | |
| 1775 | 14 | F1775V, p.F1775LfsX15, |
| 1484 | 15 | |
| 1497 | 8 | |
| 1490 | 6 | |
| 1790 | 14 | D1790N, D1790G, p.D1790del, |
| 1483 | 13 | Q1483H, Q1483H, |
| 1494 | 8 | |
| 1489 | 6 | E1489D, E1489D, |
| 1782 | 9 |