SCN5A Variant W1684R
Summary of observed carriers, functional annotations, and structural context for SCN5A W1684R. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
7%
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 (%) |
|---|---|---|---|---|---|
| 0.2 | 0.117 | 0.57 | 0.562 | 9 | 0 |
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 |
|---|---|---|
| 333 | 13 | c.998+1G>A, c.998+5G>A, |
| 326 | 15 | |
| 1741 | 10 | D1741N, D1741Y, D1741E, D1741E, |
| 1715 | 12 | |
| 1687 | 8 | |
| 1743 | 13 | G1743R, G1743R, G1743E |
| 334 | 14 | c.999-424_1338+81del, |
| 1681 | 11 | c.5040_5042delTTAinsC, Y1681F, |
| 1694 | 12 | |
| 1695 | 11 | Q1695X, |
| 1716 | 12 | p.L1716SfsX71, |
| 1688 | 5 | |
| 1684 | 0 | W1684R, W1684R, |
| 1692 | 10 | |
| 1721 | 15 | |
| 1742 | 14 | |
| 1693 | 9 | |
| 1699 | 13 | |
| 379 | 13 | |
| 1680 | 12 | A1680T, A1680P, |
| 1703 | 14 | |
| 1719 | 9 | |
| 1690 | 5 | c.5068_5070delGA, D1690N, |
| 324 | 13 | |
| 383 | 12 | |
| 1683 | 7 | |
| 1718 | 12 | S1718R, S1718R, S1718R, |
| 1689 | 6 | D1689N, |
| 1739 | 12 | R1739W, R1739Q, |
| 1717 | 15 | L1717P, |
| 1682 | 9 | |
| 336 | 14 | P336L, |
| 1686 | 8 | |
| 1740 | 13 | G1740R, G1740R, |
| 1691 | 10 | |
| 1720 | 12 | c.5157delC, |
| 1679 | 14 | |
| 1685 | 6 |