SCN5A Variant Q1909R
Summary of observed carriers, functional annotations, and structural context for SCN5A Q1909R. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
47%
2/11 effective observations
Estimated BrS1 penetrance
8%
0/11 effective observations
Total carriers
1
0 BrS1 · 1 LQT3 · 0 unaffected
Variant features alone are equivalent to phenotyping 0 individuals for Brugada syndrome and 1 individuals for LQT3.
In silico predictors
| PROVEAN | PolyPhen-2 | BLAST-PSSM | REVEL | Penetrance Density BrS (%) | Penetrance Density LQT3 (%) |
|---|---|---|---|---|---|
| -3.7 | 1 | -0.27 | 0.987 | 1 | 50 |
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 |
|---|---|---|---|---|---|---|---|
| 25904541 | 2015 | 1 | 1 | 0 | 0 | ||
| 25757662 | 2015 | 1 | 0 | 0 | 1 | SIDS | |
| 15840476 | 2005 | 1 | 1 | 0 | 0 | ||
| Literature, cohort, and gnomAD | – | 1 | 0 | 1 | 0 | – | |
| Variant features alone | – | 15 | 14 | 1 | 0 | – | – |
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) |
|---|---|---|---|---|---|---|
| 28087622 | 2017 | HEK | 90 | -3.3 | -5.6 | 222 |
| 15840476 | 2005 | |||||
| 25370050 | 2014 | HEK | 8.5 | 2.4 | ||
| 28734073 | 2017 | HEK | ||||
| 25757662 | 2015 | HEK | 81 | -8 | -0.6 | 202 |
| 25904541 | 2015 | HEK | 58 | 4 | 7 | 371 |
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 |
|---|---|---|
| 1894 | 15 | |
| 1895 | 14 | T1895I, |
| 1896 | 14 | L1896P, p.L1896PfsX47, |
| 1897 | 13 | R1897Y, R1897Q, R1897W, |
| 1898 | 13 | R1898C, R1898H |
| 1899 | 12 | |
| 1900 | 11 | |
| 1901 | 11 | E1901K, E1901Q, |
| 1902 | 10 | E1902A, |
| 1903 | 9 | V1903M, |
| 1904 | 8 | S1904L, |
| 1905 | 8 | |
| 1906 | 7 | M1906T, M1906V, |
| 1907 | 5 | |
| 1908 | 4 | I1908V, |
| 1909 | 0 | Q1909R, |
| 1910 | 4 | R1910K, |
| 1911 | 5 | |
| 1912 | 7 | |
| 1913 | 8 | R1913S, R1913H, R1913C, |
| 1914 | 8 | R1914G, |
| 1915 | 9 | H1915P, H1915Y, H1915N, H1915Q, |
| 1916 | 10 | |
| 1917 | 11 | |
| 1918 | 11 | |
| 1919 | 12 | R1919C, R1919H, |
| 1920 | 13 | S1920C, |
| 1921 | 13 | |
| 1922 | 14 | K1922R, K1922N, |
| 1923 | 14 | H1923D, H1923Y, |
| 1924 | 15 | A1924T, |