SCN5A Variant A1698T
Summary of observed carriers, functional annotations, and structural context for SCN5A A1698T. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
3%
0/14 effective observations
Estimated BrS1 penetrance
24%
3/14 effective observations
Total carriers
4
1 BrS1 · 0 LQT3 · 3 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 (%) |
|---|---|---|---|---|---|
| -2.43 | 1 | -1.6 | 0.872 | 25 | 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 | ||
| 29325976 | 2018 | 1 | 0 | 1 | 0 | ||
| Literature, cohort, and gnomAD | – | 4 | 3 | 0 | 1 | – | |
| Variant features alone | – | 15 | 13 | 0 | 2 | – | – |
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.
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+5G>A, c.998+1G>A, |
| 1702 | 6 | |
| 387 | 6 | |
| 385 | 14 | A385T, |
| 391 | 13 | |
| 330 | 11 | S330F, |
| 388 | 10 | I388S, |
| 1698 | 0 | A1698T, |
| 1220 | 13 | G1220E, |
| 1673 | 11 | |
| 1675 | 13 | |
| 1666 | 15 | |
| 332 | 12 | A332T, |
| 1707 | 14 | |
| 1694 | 9 | |
| 1704 | 10 | L1704H, |
| 1226 | 11 | |
| 1706 | 12 | Q1706H, Q1706H, |
| 1695 | 9 | Q1695X, |
| 1716 | 15 | p.L1716SfsX71, |
| 1688 | 14 | |
| 1669 | 11 | |
| 1671 | 15 | |
| 329 | 14 | |
| 1221 | 14 | A1221V, |
| 1668 | 10 | M1668T, |
| 1676 | 9 | M1676I, M1676I, M1676I, M1676T, |
| 1692 | 9 | |
| 386 | 11 | G386E, G386R, G386R, |
| 1219 | 15 | S1219N, |
| 1672 | 9 | S1672Y, |
| 1693 | 8 | |
| 378 | 12 | |
| 1699 | 4 | |
| 331 | 8 | |
| 1665 | 12 | |
| 379 | 13 | |
| 1680 | 14 | A1680P, A1680T, |
| 1703 | 8 | |
| 1701 | 5 | M1701I, M1701I, M1701I, |
| 1228 | 10 | Y1228F, Y1228H, Y1228C, |
| 1690 | 13 | D1690N, c.5068_5070delGA, |
| 1223 | 9 | c.3667delG, |
| 1697 | 4 | |
| 389 | 13 | Y389X, Y389H, |
| 1222 | 14 | p.L1222LfsX7, L1222R, |
| 1227 | 11 | |
| 393 | 14 | |
| 390 | 9 | |
| 394 | 14 | |
| 383 | 14 | |
| 1708 | 15 | T1708I, |
| 382 | 11 | |
| 1696 | 5 | |
| 1705 | 10 | |
| 1689 | 13 | D1689N, |
| 1700 | 5 | |
| 1677 | 15 | |
| 1224 | 10 | |
| 1670 | 14 | |
| 381 | 15 | c.1140+1G>A, c.1141-3C>A, |
| 1225 | 14 | E1225K, G1225K, |
| 1691 | 9 | |
| 1679 | 14 | |
| 1667 | 15 | V1667I, |