SCN5A Variant H1923Y
Summary of observed carriers, functional annotations, and structural context for SCN5A H1923Y. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
7%
0/11 effective observations
Estimated BrS1 penetrance
24%
2/11 effective observations
Total carriers
1
0 BrS1 · 0 LQT3 · 1 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 (%) |
|---|---|---|---|---|---|
| -1.48 | 0.01 | -2 | 0.555 | 30 | 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 | – | 1 | 1 | 0 | 0 | – | |
| Variant features alone | – | 15 | 13 | 0 | 2 | – | – |
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 |
|---|---|---|
| 1908 | 15 | I1908V, |
| 1909 | 14 | Q1909R, |
| 1910 | 14 | R1910K, |
| 1911 | 13 | |
| 1912 | 13 | |
| 1913 | 12 | R1913C, R1913H, R1913S, |
| 1914 | 11 | R1914G, |
| 1915 | 11 | H1915P, H1915Y, H1915Q, H1915N, |
| 1916 | 10 | |
| 1917 | 9 | |
| 1918 | 8 | |
| 1919 | 8 | R1919H, R1919C |
| 1920 | 7 | S1920C, |
| 1921 | 5 | |
| 1922 | 4 | K1922N, K1922R, |
| 1923 | 0 | H1923D, H1923Y, |
| 1924 | 4 | A1924T, |
| 1925 | 5 | p.S1925CfsX20, S1925F, |
| 1926 | 7 | |
| 1927 | 8 | L1927P, |
| 1928 | 8 | F1928V, |
| 1929 | 9 | R1929H, R1929C, |
| 1930 | 10 | Q1930H, |
| 1931 | 11 | |
| 1932 | 11 | A1932V, |
| 1933 | 12 | G1933D, G1933A, G1933V, |
| 1934 | 13 | |
| 1935 | 13 | G1935S, |
| 1936 | 14 | |
| 1937 | 14 | S1937A, |
| 1938 | 15 | E1938K, E1938X, |