SCN5A Variant L407P
Summary of observed carriers, functional annotations, and structural context for SCN5A L407P. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
49%
2/10 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 2 individuals for LQT3.
In silico predictors
| PROVEAN | PolyPhen-2 | BLAST-PSSM | REVEL | Penetrance Density BrS (%) | Penetrance Density LQT3 (%) |
|---|---|---|---|---|---|
| NA | NA | NA | 0.992 | 14 | 65 |
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 | 12 | 2 | 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 |
|---|---|---|
| 403 | 8 | |
| 414 | 10 | M414V, |
| 1643 | 10 | I1643L, |
| 404 | 5 | L404V, L404Q, |
| 1778 | 13 | |
| 1773 | 12 | |
| 1765 | 15 | |
| 249 | 11 | K249X, |
| 247 | 13 | V247L, V247L, |
| 1653 | 11 | |
| 254 | 9 | |
| 1771 | 7 | I1771T, |
| 401 | 10 | S401P, |
| 1652 | 13 | M1652T, M1652R, |
| 1777 | 14 | V1777M, V1777L, V1777L, |
| 371 | 15 | Q371E, |
| 250 | 8 | |
| 409 | 7 | L409P, L409V, |
| 928 | 10 | L928P, |
| 1650 | 8 | L1650F, |
| 260 | 12 | |
| 366 | 14 | |
| 933 | 14 | |
| 258 | 13 | V258A, |
| 246 | 12 | |
| 935 | 14 | L935P, |
| 1779 | 12 | T1779M, |
| 412 | 9 | V412D, |
| 924 | 13 | V924I, |
| 1470 | 15 | |
| 927 | 14 | N927S, N927K, N927K, |
| 1466 | 15 | c.4396_4397insG, |
| 1776 | 11 | |
| 369 | 11 | M369K, |
| 1767 | 12 | Y1767C, |
| 1654 | 13 | |
| 1648 | 13 | |
| 1769 | 12 | |
| 402 | 11 | F402L, F402L, F402L, |
| 415 | 13 | A415T, |
| 1649 | 9 | A1649V, |
| 1768 | 10 | I1768V, |
| 1774 | 11 | c.5321_5324dupACTT, N1774D, |
| 1644 | 15 | R1644C, R1644H, R1644L, |
| 256 | 9 | |
| 399 | 13 | |
| 397 | 15 | I397T, I397V, I397F, |
| 405 | 7 | |
| 1657 | 13 | |
| 261 | 14 | |
| 255 | 12 | |
| 1772 | 8 | L1772V, |
| 1645 | 12 | T1645M, |
| 251 | 11 | |
| 410 | 5 | A410V, |
| 1770 | 12 | I1770V, |
| 929 | 12 | |
| 1651 | 13 | |
| 259 | 14 | |
| 413 | 10 | A413T, A413E, |
| 408 | 5 | |
| 253 | 7 | |
| 407 | 0 | |
| 936 | 14 | |
| 1775 | 7 | F1775V, p.F1775LfsX15, |
| 370 | 14 | T370M, |
| 1642 | 11 | G1642E, |
| 406 | 6 | N406K, N406K, N406S, |
| 252 | 11 | |
| 411 | 6 | V411M, |
| 932 | 11 | |
| 398 | 14 | |
| 1647 | 9 | |
| 257 | 9 | |
| 400 | 10 | G400R, G400E, G400A, G400R, |
| 1646 | 7 |