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, |