SCN5A Variant P1048S
Summary of observed carriers, functional annotations, and structural context for SCN5A P1048S. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
11%
0/11 effective observations
Estimated BrS1 penetrance
23%
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 (%) |
|---|---|---|---|---|---|
| -7.58 | 0.99 | 1.37 | 0.647 | 32 | 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 |
|---|---|---|
| 1033 | 15 | Q1033R, |
| 1034 | 14 | P1034T, |
| 1035 | 14 | G1035V, |
| 1036 | 13 | |
| 1037 | 13 | |
| 1038 | 12 | |
| 1039 | 11 | |
| 1040 | 11 | G1040R, G1040R, |
| 1041 | 10 | D1041N, D1041G, |
| 1042 | 9 | |
| 1043 | 8 | E1043K, |
| 1044 | 8 | |
| 1045 | 7 | V1045M, |
| 1046 | 5 | |
| 1047 | 4 | c.3140_3141dupTG, |
| 1048 | 0 | P1048S, c.3142_3143insTG, p.P1048SfsX96, |
| 1049 | 4 | |
| 1050 | 5 | A1050T, p.A1050DfsX9, p.A1050CfsX9, |
| 1051 | 7 | V1051A, |
| 1052 | 8 | p.A1052CfsX7, A1052D, |
| 1053 | 8 | E1053K, |
| 1054 | 9 | |
| 1055 | 10 | D1055G, |
| 1056 | 11 | T1056A, |
| 1057 | 11 | |
| 1058 | 12 | c.3171_3172delTGinsA, |
| 1059 | 13 | Q1059X, |
| 1060 | 13 | |
| 1061 | 14 | E1061D, E1061D, |
| 1062 | 14 | D1062H, |
| 1063 | 15 | E1063G |