SCN5A Variant R1898C
Summary of observed carriers, functional annotations, and structural context for SCN5A R1898C. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
2%
0/23 effective observations
Estimated BrS1 penetrance
17%
3/23 effective observations
Total carriers
13
2 BrS1 · 0 LQT3 · 11 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 (%) |
|---|---|---|---|---|---|
| -5.73 | 0.979 | -2.71 | 0.814 | 13 | 2 |
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 |
|---|---|---|---|---|---|---|---|
| 26173111 | 2015 | 1 | 0 | 1 | 0 | ||
| 27707468 | 2016 | 1 | 0 | 1 | 0 | ||
| 26746457 | 2016 | 1 | 0 | 0 | 0 | ||
| Literature, cohort, and gnomAD | – | 13 | 11 | 0 | 2 | – | |
| Variant features alone | – | 15 | 14 | 0 | 1 | – | – |
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 |
|---|---|---|
| 1883 | 15 | |
| 1884 | 14 | P1884L, |
| 1885 | 14 | |
| 1886 | 13 | |
| 1887 | 13 | |
| 1888 | 12 | |
| 1889 | 11 | Y1889C, |
| 1890 | 11 | E1890K, |
| 1891 | 10 | |
| 1892 | 9 | |
| 1893 | 8 | c.5676delC, |
| 1894 | 8 | |
| 1895 | 7 | T1895I, |
| 1896 | 5 | p.L1896PfsX47, L1896P, |
| 1897 | 4 | R1897Y, R1897W, R1897Q, |
| 1898 | 0 | R1898H, R1898C, |
| 1899 | 4 | |
| 1900 | 5 | |
| 1901 | 7 | E1901K, E1901Q, |
| 1902 | 8 | E1902A, |
| 1903 | 8 | V1903M, |
| 1904 | 9 | S1904L, |
| 1905 | 10 | |
| 1906 | 11 | M1906V, M1906T, |
| 1907 | 11 | |
| 1908 | 12 | I1908V, |
| 1909 | 13 | Q1909R, |
| 1910 | 13 | R1910K, |
| 1911 | 14 | |
| 1912 | 14 | |
| 1913 | 15 | R1913C, R1913H, R1913S, |