SCN5A Variant N420I
Summary of observed carriers, functional annotations, and structural context for SCN5A N420I. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
15%
0/10 effective observations
Estimated BrS1 penetrance
13%
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 | 0.846 | 9 | 16 |
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 | 11 | M414V, |
| 939 | 11 | L939F, |
| 937 | 9 | |
| 839 | 14 | L839P, |
| 842 | 13 | |
| 943 | 13 | S943N, |
| 240 | 12 | V240M, |
| 418 | 8 | E418K, |
| 237 | 11 | |
| 234 | 15 | P234S, |
| 417 | 5 | |
| 934 | 14 | |
| 933 | 11 | |
| 246 | 13 | |
| 935 | 14 | L935P, |
| 412 | 12 | V412D, |
| 245 | 13 | Q245K, |
| 244 | 14 | |
| 415 | 9 | A415T, |
| 940 | 7 | S940N, |
| 420 | 0 | |
| 938 | 13 | |
| 241 | 10 | |
| 235 | 11 | c.703+1G>A, G235R, G235R, c.704-1G>C, |
| 942 | 14 | |
| 419 | 5 | Q419X, |
| 423 | 6 | |
| 834 | 14 | N834D, |
| 837 | 13 | |
| 239 | 10 | I239V, I239V , |
| 1780 | 15 | E1780G |
| 242 | 9 | A242D, |
| 416 | 5 | Y416C, |
| 413 | 10 | A413T, A413E, |
| 841 | 13 | p.N841TfsX2, N841K, N841K, |
| 236 | 13 | |
| 941 | 10 | S941N, S941F, |
| 936 | 10 | |
| 238 | 6 | |
| 838 | 10 | |
| 422 | 6 | |
| 421 | 5 | |
| 411 | 14 | V411M, |
| 243 | 13 | |
| 835 | 13 | S835A, S835L, |