SCN5A Variant A415P
Summary of observed carriers, functional annotations, and structural context for SCN5A A415P. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
13%
0/10 effective observations
Estimated BrS1 penetrance
14%
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 | 0.925 | 10 | 14 |
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 | 4 | M414V, |
| 939 | 12 | L939F, |
| 937 | 12 | |
| 1778 | 14 | |
| 1773 | 15 | |
| 842 | 14 | |
| 249 | 7 | K249X, |
| 247 | 10 | V247L, V247L, |
| 240 | 11 | V240M, |
| 1777 | 15 | V1777M, V1777L, V1777L, |
| 418 | 5 | E418K, |
| 250 | 11 | |
| 409 | 10 | L409V, L409P, |
| 237 | 13 | |
| 928 | 14 | L928P, |
| 417 | 7 | |
| 934 | 14 | |
| 933 | 9 | |
| 246 | 6 | |
| 935 | 13 | L935P, |
| 1779 | 11 | T1779M, |
| 412 | 6 | V412D, |
| 245 | 6 | Q245K, |
| 1776 | 11 | |
| 244 | 10 | |
| 415 | 0 | A415T, |
| 940 | 12 | S940N, |
| 420 | 9 | |
| 248 | 11 | |
| 938 | 15 | |
| 241 | 8 | |
| 419 | 7 | Q419X, |
| 930 | 12 | c.2787+17_2787+18insACACACACACACACACACACACA, c.2788-6C>T, |
| 423 | 12 | |
| 1772 | 12 | L1772V, |
| 239 | 10 | I239V, I239V , |
| 251 | 14 | |
| 410 | 8 | A410V, |
| 1780 | 12 | E1780G |
| 242 | 6 | A242D, |
| 929 | 11 | |
| 416 | 6 | Y416C, |
| 413 | 5 | A413T, A413E, |
| 408 | 11 | |
| 253 | 14 | |
| 407 | 13 | |
| 1783 | 14 | |
| 936 | 9 | |
| 238 | 10 | |
| 422 | 10 | |
| 1775 | 11 | F1775V, p.F1775LfsX15, |
| 1642 | 15 | G1642E, |
| 421 | 10 | |
| 406 | 15 | N406S, N406K, N406K, |
| 252 | 15 | |
| 411 | 6 | V411M, |
| 243 | 9 | |
| 932 | 11 | |
| 931 | 15 | |
| 1646 | 15 | |
| 1782 | 14 |