SCN5A Variant T1709R
Summary of observed carriers, functional annotations, and structural context for SCN5A T1709R. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
0%
0/11 effective observations
Estimated BrS1 penetrance
55%
6/11 effective observations
Total carriers
1
1 BrS1 · 0 LQT3 · 0 unaffected
Variant features alone are equivalent to phenotyping 5 individuals for Brugada syndrome and 0 individuals for LQT3.
In silico predictors
| PROVEAN | PolyPhen-2 | BLAST-PSSM | REVEL | Penetrance Density BrS (%) | Penetrance Density LQT3 (%) |
|---|---|---|---|---|---|
| -5.55 | 1 | -5.01 | 0.979 | 73 | 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 |
|---|---|---|---|---|---|---|---|
| 20129283 | 2010 | 1 | 0 | 1 | 0 | ||
| Literature, cohort, and gnomAD | – | 1 | 0 | 0 | 1 | – | |
| Variant features alone | – | 15 | 10 | 0 | 5 | – | – |
Totals may differ from individual publications due to duplicate patients removed during curation.
Functional data
Peak and late/persistent current values are relative to wild-type (100% indicates no change). V1/2 activation and inactivation denote the membrane potentials (mV) at which half-maximal current is achieved.
| PubMed ID | Year | Cell Type | Peak Current (% WT) | V1/2 Activation (mV) | V1/2 Inactivation (mV) | Late/Persistent Current (% WT) |
|---|---|---|---|---|---|---|
| 20129283 | 2010 |
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 |
|---|---|---|
| 403 | 15 | |
| 1702 | 12 | |
| 896 | 15 | C896S, C896S, |
| 1417 | 10 | |
| 1765 | 11 | |
| 396 | 12 | V396A, V396L, |
| 1757 | 13 | |
| 1715 | 14 | |
| 372 | 11 | |
| 401 | 10 | S401P, |
| 1756 | 10 | I1756V, |
| 1764 | 8 | c.5290delG, V1764F, |
| 371 | 6 | Q371E, |
| 1711 | 5 | c.5131delG, |
| 1754 | 15 | |
| 1707 | 7 | |
| 1704 | 9 | L1704H, |
| 1706 | 7 | Q1706H, Q1706H, |
| 1716 | 12 | p.L1716SfsX71, |
| 1714 | 14 | D1714G, |
| 376 | 14 | R376H, R376C, |
| 1671 | 15 | |
| 897 | 13 | G897R, G897E, G897R, |
| 1762 | 13 | I1762M, p.I1762del, |
| 1668 | 11 | M1668T, |
| 1692 | 15 | |
| 369 | 12 | M369K, |
| 1753 | 15 | T1753A, |
| 1767 | 12 | Y1767C, |
| 1660 | 14 | I1660S, I1660V, |
| 378 | 11 | |
| 1418 | 12 | |
| 402 | 9 | F402L, F402L, F402L, |
| 1766 | 14 | M1766V, M1766T, M1766L, M1766L, |
| 1665 | 15 | |
| 373 | 10 | |
| 1768 | 13 | I1768V, |
| 1712 | 9 | G1712S, G1712C, |
| 379 | 13 | |
| 1703 | 11 | |
| 898 | 13 | |
| 1663 | 15 | |
| 399 | 14 | |
| 397 | 8 | I397F, I397V, I397T, |
| 405 | 13 | |
| 1462 | 14 | |
| 1759 | 8 | S1759C, |
| 1709 | 0 | T1709R, T1709M, p.T1709del, |
| 1701 | 13 | M1701I, M1701I, M1701I, |
| 1420 | 15 | G1420V, G1420R, G1420P, G1420D, |
| 1758 | 13 | I1758V, p.I1758del, |
| 1755 | 10 | |
| 395 | 15 | |
| 393 | 11 | |
| 1713 | 8 | |
| 390 | 14 | |
| 394 | 11 | |
| 1708 | 4 | T1708I, |
| 374 | 7 | W374G, |
| 1705 | 8 | |
| 1700 | 15 | |
| 1717 | 15 | L1717P, |
| 367 | 13 | R367L, R367C, R367H, |
| 1763 | 11 | V1763L, V1763M, V1763L, |
| 1416 | 14 | A1416E, c.4245+2T>A, c.4245+1G>C, c.4245+1G>A, A1416G, |
| 1760 | 7 | |
| 370 | 11 | T370M, |
| 1752 | 12 | |
| 1661 | 13 | G1661R, G1661R, G1661E, |
| 1761 | 11 | L1761F, L1761H, c.5280delG, |
| 375 | 10 | |
| 406 | 14 | N406K, N406K, N406S, |
| 368 | 10 | |
| 1710 | 4 | S1710L, |
| 377 | 13 | |
| 398 | 11 | |
| 400 | 13 | G400A, G400R, G400E, G400R, |
| 1419 | 10 | K1419E, |
| 1667 | 13 | V1667I, |
| 1414 | 14 | Q1414H, Q1414H, |
| 1664 | 10 |