SCN5A Variant K1024R
Summary of observed carriers, functional annotations, and structural context for SCN5A K1024R. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
4%
0/11 effective observations
Estimated BrS1 penetrance
8%
0/11 effective observations
Total carriers
1
0 BrS1 · 0 LQT3 · 1 unaffected
Variant features alone are equivalent to phenotyping 0 individuals for Brugada syndrome and 0 individuals for LQT3.
In silico predictors
| PROVEAN | PolyPhen-2 | BLAST-PSSM | REVEL | Penetrance Density BrS (%) | Penetrance Density LQT3 (%) |
|---|---|---|---|---|---|
| -0.81 | 0.993 | 0.82 | 0.574 | 1 | 3 |
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 | 15 | 0 | 0 | – | – |
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 |
|---|---|---|
| 1009 | 15 | |
| 1010 | 14 | |
| 1011 | 14 | P1011S, P1011L, |
| 1012 | 13 | |
| 1013 | 13 | |
| 1014 | 12 | P1014S, |
| 1015 | 11 | E1015K, p.G1015DfsX14, |
| 1016 | 11 | T1016M, c.3045_3046delGA, |
| 1017 | 10 | |
| 1018 | 9 | K1018E, |
| 1019 | 8 | |
| 1020 | 8 | |
| 1021 | 7 | P1021S, |
| 1022 | 5 | |
| 1023 | 4 | R1023P, R1023H, R1023C, |
| 1024 | 0 | K1024R, |
| 1025 | 4 | E1025A, |
| 1026 | 5 | |
| 1027 | 7 | R1027P, R1027W, R1027Q, |
| 1028 | 8 | |
| 1029 | 8 | E1029K, |
| 1030 | 9 | |
| 1031 | 10 | p.G1031fsX27, |
| 1032 | 11 | E1032D, E1032D, E1032K, |
| 1033 | 11 | Q1033R, |
| 1034 | 12 | P1034T, |
| 1035 | 13 | G1035V, |
| 1036 | 13 | |
| 1037 | 14 | |
| 1038 | 14 | |
| 1039 | 15 |