SCN5A Variant A1050T
Summary of observed carriers, functional annotations, and structural context for SCN5A A1050T. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
4%
0/12 effective observations
Estimated BrS1 penetrance
9%
1/12 effective observations
Total carriers
2
0 BrS1 · 0 LQT3 · 2 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 (%) |
|---|---|---|---|---|---|
| -3.81 | 0.999 | 0.58 | 0.73 | 6 | 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 | – | 2 | 2 | 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 |
|---|---|---|
| 1035 | 15 | G1035V, |
| 1036 | 14 | |
| 1037 | 14 | |
| 1038 | 13 | |
| 1039 | 13 | |
| 1040 | 12 | G1040R, G1040R, |
| 1041 | 11 | D1041N, D1041G, |
| 1042 | 11 | |
| 1043 | 10 | E1043K, |
| 1044 | 9 | |
| 1045 | 8 | V1045M, |
| 1046 | 8 | |
| 1047 | 7 | c.3140_3141dupTG, |
| 1048 | 5 | c.3142_3143insTG, p.P1048SfsX96, P1048S, |
| 1049 | 4 | |
| 1050 | 0 | p.A1050DfsX9, A1050T, p.A1050CfsX9, |
| 1051 | 4 | V1051A, |
| 1052 | 5 | A1052D, p.A1052CfsX7 |
| 1053 | 7 | E1053K, |
| 1054 | 8 | |
| 1055 | 8 | D1055G, |
| 1056 | 9 | T1056A, |
| 1057 | 10 | |
| 1058 | 11 | c.3171_3172delTGinsA, |
| 1059 | 11 | Q1059X, |
| 1060 | 12 | |
| 1061 | 13 | E1061D, E1061D, |
| 1062 | 13 | D1062H, |
| 1063 | 14 | E1063G, |
| 1064 | 14 | p.E1064del, |
| 1065 | 15 |