SCN5A Variant Y403S
Summary of observed carriers, functional annotations, and structural context for SCN5A Y403S. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
32%
1/10 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 1 individuals for LQT3.
In silico predictors
| PROVEAN | PolyPhen-2 | BLAST-PSSM | REVEL | Penetrance Density BrS (%) | Penetrance Density LQT3 (%) |
|---|---|---|---|---|---|
| NA | NA | NA | 0.978 | 9 | 41 |
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 | 13 | 1 | 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 | 0 | |
| 1659 | 13 | |
| 1643 | 14 | I1643L, |
| 404 | 6 | L404Q, L404V, |
| 1773 | 14 | |
| 1765 | 13 | |
| 396 | 10 | V396L, V396A, |
| 1653 | 8 | |
| 254 | 14 | |
| 1771 | 7 | I1771T, |
| 401 | 7 | S401P, |
| 1652 | 12 | M1652R, M1652T, |
| 1634 | 14 | L1634P, |
| 1764 | 11 | V1764F, c.5290delG, |
| 371 | 13 | Q371E, |
| 409 | 12 | L409V, L409P, |
| 928 | 15 | L928P, |
| 1650 | 6 | L1650F, |
| 260 | 10 | |
| 366 | 15 | |
| 1656 | 11 | |
| 365 | 15 | |
| 369 | 10 | M369K, |
| 1767 | 7 | Y1767C, |
| 1660 | 11 | I1660S, I1660V, |
| 1654 | 8 | |
| 1648 | 13 | |
| 1769 | 11 | |
| 402 | 6 | F402L, F402L, F402L, |
| 1766 | 14 | M1766V, M1766L, M1766L, M1766T, |
| 1649 | 10 | A1649V, |
| 1768 | 9 | I1768V, |
| 1774 | 12 | N1774D, c.5321_5324dupACTT, |
| 256 | 11 | |
| 399 | 6 | |
| 397 | 9 | I397F, I397T, I397V, |
| 405 | 8 | |
| 1657 | 7 | |
| 261 | 13 | |
| 1709 | 15 | p.T1709del, T1709R, T1709M, |
| 1772 | 11 | L1772V, |
| 1645 | 15 | T1645M, |
| 395 | 11 | |
| 394 | 12 | |
| 410 | 12 | A410V, |
| 1770 | 10 | I1770V, |
| 1658 | 10 | |
| 264 | 13 | |
| 1651 | 11 | |
| 259 | 14 | |
| 408 | 11 | |
| 253 | 12 | |
| 407 | 8 | |
| 1763 | 14 | V1763L, V1763L, V1763M, |
| 263 | 14 | V263I, |
| 1775 | 12 | p.F1775LfsX15, F1775V, |
| 370 | 13 | T370M, |
| 1661 | 12 | G1661R, G1661R, G1661E, |
| 1655 | 11 | |
| 406 | 7 | N406K, N406S, N406K, |
| 368 | 13 | |
| 411 | 14 | V411M, |
| 398 | 7 | |
| 1647 | 10 | |
| 257 | 11 | |
| 400 | 5 | G400A, G400E, G400R, G400R, |
| 1646 | 11 | |
| 1664 | 14 |