SCN5A Variant Q1439H
Summary of observed carriers, functional annotations, and structural context for SCN5A Q1439H. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
2%
0/11 effective observations
Estimated BrS1 penetrance
20%
2/11 effective observations
Total carriers
1
0 BrS1 · 0 LQT3 · 1 unaffected
Variant features alone are equivalent to phenotyping 2 individuals for Brugada syndrome and 0 individuals for LQT3.
In silico predictors
| PROVEAN | PolyPhen-2 | BLAST-PSSM | REVEL | Penetrance Density BrS (%) | Penetrance Density LQT3 (%) |
|---|---|---|---|---|---|
| -2.08 | 0.486 | -1.25 | 0.571 | 23 | 2 |
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 | 0 | 2 | – | – |
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 |
|---|---|---|
| 1386 | 9 | |
| 1430 | 6 | D1430N, |
| 1426 | 10 | |
| 1445 | 14 | Y1445H, |
| 1361 | 11 | |
| 1444 | 12 | L1444I, |
| 1440 | 7 | W1440X, |
| 1382 | 7 | S1382I, |
| 1395 | 13 | |
| 1380 | 9 | p.N1380del, N1380K, N1380K, |
| 1429 | 9 | |
| 1442 | 5 | Y1442C, Y1442N, |
| 1358 | 15 | G1358W, G1358R, G1358R, |
| 1362 | 9 | R1362S, R1362S, c.4083delG, |
| 1433 | 10 | G1433R, G1433W, G1433V, G1433R, |
| 1438 | 5 | P1438L, |
| 1388 | 12 | |
| 1387 | 8 | L1387F, L1387F, |
| 1437 | 6 | |
| 876 | 15 | |
| 1384 | 10 | C1384Y, |
| 1431 | 8 | S1431C, |
| 1383 | 7 | Q1383X, |
| 1359 | 12 | K1359N, K1359M, K1359N, |
| 1434 | 14 | c.4299G>A, c.4299_4300insG, c.4299delG, c.4299+28C>T, c.4299+1G>T, c.4299+1delG, c.4300-2A>T, c.4299+2T>A, c.4300-1G>A, Y1434X, |
| 1356 | 15 | c.4066_4068delTT, |
| 1381 | 11 | |
| 1435 | 14 | |
| 1360 | 13 | F1360C, |
| 1425 | 15 | |
| 1427 | 10 | A1427S, A1427E, |
| 1385 | 13 | |
| 1446 | 15 | |
| 1432 | 6 | R1432S, R1432G, R1432S, |
| 1389 | 15 | |
| 1439 | 0 | Q1439H, Q1439H, Q1439R, |
| 1364 | 13 | I1364V, |
| 878 | 13 | R878C, R878L, R878H, |
| 1443 | 9 | N1443S, |
| 1441 | 7 | E1441Q, |
| 1379 | 14 | |
| 1428 | 11 | A1428V, A1428S |
| 1363 | 11 | C1363Y, |
| 1436 | 9 |