SCN5A Variant C1539F
Summary of observed carriers, functional annotations, and structural context for SCN5A C1539F. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
12%
0/11 effective observations
Estimated BrS1 penetrance
9%
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 0 individuals for LQT3.
In silico predictors
| PROVEAN | PolyPhen-2 | BLAST-PSSM | REVEL | Penetrance Density BrS (%) | Penetrance Density LQT3 (%) |
|---|---|---|---|---|---|
| -9.39 | 0.998 | 1.22 | 0.84 | 1 | 1 |
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 | 0 | 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 |
|---|---|---|
| 266 | 12 | L266H, |
| 1544 | 10 | T1544P, |
| 1627 | 10 | |
| 1567 | 10 | F1567L, F1567L, F1567L, |
| 1536 | 6 | |
| 1538 | 4 | |
| 1531 | 13 | |
| 1566 | 14 | |
| 1635 | 13 | |
| 1568 | 15 | |
| 1634 | 13 | L1634P |
| 1543 | 7 | V1543L, V1543L, V1543A, |
| 1534 | 9 | |
| 1542 | 6 | |
| 260 | 14 | |
| 1571 | 11 | F1571C, |
| 1564 | 14 | |
| 1570 | 13 | p.1570_F1571insI, I1570V, p.I1570dup, |
| 258 | 13 | V258A, |
| 1529 | 15 | |
| 1546 | 10 | M1546T, |
| 1545 | 10 | |
| 1630 | 7 | I1630V, I1630R, |
| 1532 | 10 | V1532I, V1532F, |
| 1626 | 11 | R1626C, R1626H, R1626P, R1626L, |
| 267 | 15 | |
| 1625 | 15 | |
| 262 | 11 | S262G, |
| 256 | 15 | |
| 1628 | 11 | |
| 1632 | 9 | R1632C, R1632H, R1632L, |
| 1539 | 0 | C1539Y, C1539F, |
| 1530 | 14 | |
| 255 | 14 | |
| 1535 | 6 | |
| 1537 | 6 | |
| 259 | 10 | |
| 1633 | 8 | |
| 1591 | 14 | W1591X, |
| 1595 | 13 | |
| 265 | 15 | A265V, |
| 1637 | 14 | |
| 1636 | 11 | |
| 358 | 14 | |
| 263 | 11 | V263I, |
| 1629 | 9 | R1629G, R1629X, R1629Q, |
| 1547 | 14 | V1547L, V1547L, |
| 1574 | 14 | c.4719C>T, E1574K, |
| 1533 | 10 | T1533I, |
| 1563 | 13 | |
| 1541 | 7 | |
| 1540 | 5 | |
| 1631 | 10 | G1631D, |
| 1598 | 15 | V1598A, |