SCN5A Variant N406H
Summary of observed carriers, functional annotations, and structural context for SCN5A N406H. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
39%
1/10 effective observations
Estimated BrS1 penetrance
20%
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 | 0.94 | 20 | 50 |
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 | 7 | |
| 414 | 13 | M414V, |
| 939 | 14 | L939F, |
| 404 | 7 | L404Q, L404V, |
| 1773 | 11 | |
| 1765 | 9 | |
| 396 | 14 | V396A, V396L, |
| 1653 | 11 | |
| 254 | 14 | |
| 1771 | 6 | I1771T, |
| 401 | 7 | S401P, |
| 1652 | 14 | M1652R, M1652T, |
| 1764 | 10 | c.5290delG, V1764F, |
| 371 | 11 | Q371E, |
| 250 | 12 | |
| 409 | 5 | L409P, L409V, |
| 928 | 10 | L928P, |
| 1650 | 10 | L1650F, |
| 260 | 14 | |
| 366 | 14 | |
| 1656 | 14 | |
| 933 | 14 | |
| 246 | 14 | |
| 935 | 10 | L935P, |
| 412 | 10 | V412D, |
| 924 | 14 | V924I, |
| 1762 | 15 | p.I1762del, I1762M, |
| 1470 | 11 | |
| 927 | 12 | N927K, N927K, N927S, |
| 1466 | 10 | c.4396_4397insG, |
| 1776 | 13 | |
| 369 | 10 | M369K, |
| 1767 | 8 | Y1767C, |
| 1660 | 13 | I1660V, I1660S, |
| 1654 | 13 | |
| 1769 | 8 | |
| 402 | 7 | F402L, F402L, F402L, |
| 1766 | 12 | M1766V, M1766T, M1766L, M1766L, |
| 415 | 15 | A415T, |
| 1649 | 12 | A1649V, |
| 1768 | 5 | I1768V, |
| 1774 | 12 | N1774D, c.5321_5324dupACTT, |
| 1473 | 14 | F1473S, F1473C, |
| 256 | 13 | |
| 399 | 12 | |
| 397 | 12 | I397T, I397F, I397V, |
| 405 | 4 | |
| 1657 | 11 | |
| 1709 | 14 | p.T1709del, T1709M, T1709R |
| 930 | 15 | c.2788-6C>T, c.2787+17_2787+18insACACACACACACACACACACACA, |
| 1772 | 7 | L1772V, |
| 410 | 7 | A410V, |
| 1770 | 9 | I1770V, |
| 929 | 13 | |
| 413 | 11 | A413E, A413T, |
| 408 | 7 | |
| 253 | 12 | |
| 407 | 6 | |
| 936 | 13 | |
| 1763 | 13 | V1763L, V1763L, V1763M, |
| 1760 | 14 | |
| 1467 | 13 | |
| 1775 | 10 | F1775V, p.F1775LfsX15, |
| 370 | 12 | T370M, |
| 923 | 15 | |
| 1469 | 13 | I1469V, |
| 406 | 0 | N406K, N406S, N406K, |
| 368 | 15 | |
| 411 | 10 | V411M, |
| 932 | 9 | |
| 398 | 11 | |
| 1647 | 14 | |
| 257 | 12 | |
| 400 | 9 | G400E, G400R, G400A, G400R, |
| 931 | 13 | |
| 1646 | 12 | |
| 1463 | 13 | N1463Y, |