SCN5A Variant E417A
Summary of observed carriers, functional annotations, and structural context for SCN5A E417A. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
12%
0/10 effective observations
Estimated BrS1 penetrance
17%
1/10 effective observations
Total carriers
0
0 BrS1 · 0 LQT3 · 0 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 (%) |
|---|---|---|---|---|---|
| NA | NA | NA | 0.789 | 17 | 12 |
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 | – | 0 | 0 | 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 |
|---|---|---|
| 414 | 7 | M414V, |
| 939 | 9 | L939F, |
| 937 | 10 | |
| 1778 | 15 | |
| 1773 | 13 | |
| 842 | 15 | |
| 249 | 13 | K249X, |
| 943 | 11 | S943N, |
| 1777 | 14 | V1777L, V1777L, V1777M, |
| 418 | 6 | E418K, |
| 409 | 12 | L409V, L409P, |
| 417 | 0 | |
| 934 | 14 | |
| 933 | 11 | |
| 1471 | 13 | |
| 246 | 12 | |
| 935 | 12 | L935P, |
| 1779 | 12 | T1779M, |
| 412 | 10 | V412D, |
| 1470 | 13 | |
| 245 | 12 | Q245K, |
| 1776 | 10 | |
| 415 | 7 | A415T, |
| 940 | 7 | S940N, |
| 420 | 5 | |
| 938 | 12 | |
| 1474 | 14 | |
| 241 | 12 | |
| 942 | 13 | |
| 419 | 7 | Q419X, |
| 423 | 10 | |
| 1772 | 12 | L1772V, |
| 239 | 12 | I239V, I239V , |
| 410 | 11 | A410V, |
| 1780 | 11 | E1780G, |
| 242 | 10 | A242D, |
| 416 | 5 | Y416C, |
| 413 | 6 | A413E, A413T, |
| 941 | 11 | S941F, S941N, |
| 1783 | 14 | |
| 936 | 8 | |
| 238 | 10 | |
| 838 | 14 | |
| 422 | 9 | |
| 1467 | 14 | |
| 1775 | 13 | p.F1775LfsX15, F1775V, |
| 421 | 5 | |
| 411 | 11 | V411M, |
| 243 | 14 | |
| 932 | 14 | |
| 1489 | 13 | E1489D, E1489D, |