SCN5A Variant K1478E
Summary of observed carriers, functional annotations, and structural context for SCN5A K1478E. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
27%
1/11 effective observations
Estimated BrS1 penetrance
8%
0/11 effective observations
Total carriers
1
0 BrS1 · 0 LQT3 · 1 unaffected
Variant features alone are equivalent to phenotyping 0 individuals for Brugada syndrome and 1 individuals for LQT3.
In silico predictors
| PROVEAN | PolyPhen-2 | BLAST-PSSM | REVEL | Penetrance Density BrS (%) | Penetrance Density LQT3 (%) |
|---|---|---|---|---|---|
| -3.69 | 0.344 | 1.84 | 0.757 | 7 | 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 | – | 1 | 1 | 0 | 0 | – | |
| Variant features alone | – | 15 | 14 | 1 | 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 |
|---|---|---|
| 1480 | 8 | c.4438-1C>T, c.4437+5G>A, |
| 1773 | 10 | |
| 943 | 14 | S943N, |
| 1486 | 11 | p.F1486del, F1486L, |
| 1472 | 11 | p.N1472del, N1472S, |
| 1777 | 11 | V1777L, V1777M, |
| 1485 | 10 | |
| 1487 | 8 | M1487K, M1487L, |
| 1492 | 8 | |
| 1477 | 6 | K1477N, |
| 1491 | 13 | Q1491H, |
| 1471 | 11 | |
| 1493 | 13 | p.K1493del, K1493R, K1493X |
| 1470 | 13 | |
| 1478 | 0 | K1478E, |
| 1776 | 13 | |
| 1329 | 15 | G1329S, |
| 1769 | 14 | |
| 1495 | 11 | Y1495S, |
| 1774 | 13 | N1774D, c.5321_5324dupACTT, |
| 1479 | 6 | |
| 1473 | 10 | F1473C, F1473S, |
| 1496 | 12 | |
| 1474 | 5 | |
| 1481 | 7 | G1481V, G1481E, G1481R, |
| 1781 | 15 | E1781G, E1781D, |
| 1772 | 15 | L1772V, |
| 1488 | 11 | T1488R, |
| 1780 | 14 | E1780G, |
| 1770 | 14 | I1770V, |
| 1482 | 5 | |
| 1322 | 12 | c.3963+2T>C, c.3963+4A>G, |
| 1326 | 13 | A1326S, |
| 1476 | 7 | Q1476X, Q1476R, |
| 1484 | 6 | |
| 1490 | 14 | |
| 1475 | 5 | Q1475L, p.Q1475NfsX6, |
| 1469 | 15 | I1469V, |
| 1483 | 7 | Q1483H, |
| 1325 | 13 | N1325S, |
| 1489 | 9 | E1489D, |