SCN5A Variant V1543A
Summary of observed carriers, functional annotations, and structural context for SCN5A V1543A. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
5%
0/12 effective observations
Estimated BrS1 penetrance
8%
0/12 effective observations
Total carriers
2
0 BrS1 · 0 LQT3 · 2 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 (%) |
|---|---|---|---|---|---|
| -3.6 | 0.303 | -1.79 | 0.87 | 2 | 10 |
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 | – | 2 | 2 | 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 |
|---|---|---|
| 266 | 9 | L266H, |
| 1544 | 4 | T1544P, |
| 270 | 12 | Q270K, |
| 1627 | 11 | |
| 1567 | 10 | F1567L, F1567L, F1567L, |
| 1536 | 10 | |
| 1549 | 13 | |
| 1538 | 9 | |
| 1566 | 14 | |
| 1556 | 13 | |
| 1543 | 0 | V1543L, V1543L, V1543A, |
| 1534 | 14 | |
| 1542 | 5 | |
| 361 | 15 | |
| 1571 | 14 | F1571C, |
| 1564 | 11 | |
| 258 | 14 | V258A, |
| 1546 | 5 | M1546T, |
| 1545 | 7 | |
| 1630 | 11 | I1630V, I1630R |
| 1626 | 11 | R1626C, R1626H, R1626P, R1626L, |
| 267 | 13 | |
| 1560 | 10 | L1560F, L1560F, |
| 262 | 10 | S262G, |
| 357 | 13 | |
| 362 | 14 | |
| 261 | 15 | |
| 1559 | 13 | I1559V, |
| 1628 | 15 | |
| 1539 | 7 | C1539Y, C1539F, |
| 269 | 12 | |
| 1535 | 13 | |
| 1537 | 10 | |
| 259 | 12 | |
| 1633 | 14 | |
| 1548 | 10 | E1548K, G1548K, |
| 265 | 12 | A265V, |
| 358 | 10 | |
| 263 | 11 | V263I, |
| 359 | 14 | A359T, p.A359PfsX12, |
| 1629 | 14 | R1629G, R1629X, R1629Q, |
| 1547 | 7 | V1547L, V1547L, |
| 1563 | 10 | |
| 1541 | 6 | |
| 1540 | 5 | |
| 268 | 15 | G268S, |
| 1561 | 14 | |
| 1623 | 14 | c.4867delC, R1623X, R1623Q, R1623L, |