SCN5A Variant Y1889C
Summary of observed carriers, functional annotations, and structural context for SCN5A Y1889C. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
3%
0/17 effective observations
Estimated BrS1 penetrance
7%
1/17 effective observations
Total carriers
7
0 BrS1 · 0 LQT3 · 7 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 (%) |
|---|---|---|---|---|---|
| -8.11 | 0.989 | -2.48 | 0.918 | 4 | 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 |
|---|---|---|---|---|---|---|---|
| Literature, cohort, and gnomAD | – | 7 | 7 | 0 | 0 | – | |
| Variant features alone | – | 15 | 14 | 0 | 1 | – | – |
Totals may differ from individual publications due to duplicate patients removed during curation.
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 |
|---|---|---|
| 1874 | 15 | |
| 1875 | 14 | M1875T, M1875K, p.M1875dup |
| 1876 | 14 | |
| 1877 | 13 | E1877K, |
| 1878 | 13 | |
| 1879 | 12 | |
| 1880 | 11 | M1880V, |
| 1881 | 11 | |
| 1882 | 10 | |
| 1883 | 9 | |
| 1884 | 8 | P1884L, |
| 1885 | 8 | |
| 1886 | 7 | |
| 1887 | 5 | |
| 1888 | 4 | |
| 1889 | 0 | Y1889C, |
| 1890 | 4 | E1890K, |
| 1891 | 5 | |
| 1892 | 7 | |
| 1893 | 8 | c.5676delC, |
| 1894 | 8 | |
| 1895 | 9 | T1895I, |
| 1896 | 10 | p.L1896PfsX47, L1896P, |
| 1897 | 11 | R1897Y, R1897W, R1897Q, |
| 1898 | 11 | R1898H, R1898C, |
| 1899 | 12 | |
| 1900 | 13 | |
| 1901 | 13 | E1901K, E1901Q, |
| 1902 | 14 | E1902A, |
| 1903 | 14 | V1903M, |
| 1904 | 15 | S1904L, |