SCN5A Variant P1506T
Summary of observed carriers, functional annotations, and structural context for SCN5A P1506T. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
22%
1/11 effective observations
Estimated BrS1 penetrance
45%
4/11 effective observations
Total carriers
1
1 BrS1 · 0 LQT3 · 0 unaffected
Variant features alone are equivalent to phenotyping 3 individuals for Brugada syndrome and 1 individuals for LQT3.
In silico predictors
| PROVEAN | PolyPhen-2 | BLAST-PSSM | REVEL | Penetrance Density BrS (%) | Penetrance Density LQT3 (%) |
|---|---|---|---|---|---|
| -7.36 | 0.999 | -3.21 | 0.934 | 55 | 30 |
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 |
|---|---|---|---|---|---|---|---|
| 23321620 | 2013 | 1 | 0 | 1 | 0 | ||
| Literature, cohort, and gnomAD | – | 1 | 0 | 0 | 1 | – | |
| Variant features alone | – | 15 | 11 | 1 | 3 | – | – |
Totals may differ from individual publications due to duplicate patients removed during curation.
Functional data
Peak and late/persistent current values are relative to wild-type (100% indicates no change). V1/2 activation and inactivation denote the membrane potentials (mV) at which half-maximal current is achieved.
| PubMed ID | Year | Cell Type | Peak Current (% WT) | V1/2 Activation (mV) | V1/2 Inactivation (mV) | Late/Persistent Current (% WT) |
|---|---|---|---|---|---|---|
| 23321620 | 2013 |
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 |
|---|---|---|
| 1850 | 8 | C1850S, C1850S, |
| 1803 | 11 | |
| 1794 | 10 | |
| 1849 | 10 | H1849R, |
| 1806 | 8 | p.Thr1806SerfsX27, |
| 1853 | 13 | I1853V, |
| 1795 | 6 | Y1795C, Y1795H, p.Y1795_E1796insD, Y1795N, |
| 1801 | 13 | |
| 1511 | 14 | |
| 1802 | 8 | |
| 1510 | 13 | |
| 1504 | 8 | K1504E, |
| 1851 | 10 | M1851I, M1851V, M1851I, M1851I, |
| 1501 | 13 | p.L1501_K1505del, L1501V, |
| 1507 | 5 | p.Q1507_P1509del, |
| 1505 | 5 | p.K1505_Q1507del, K1505N, K1505N, |
| 1509 | 9 | P1509T, |
| 1808 | 11 | |
| 1804 | 11 | |
| 1807 | 6 | c.5420dupA, |
| 1798 | 7 | W1798X, |
| 1585 | 15 | Y1585C, |
| 1854 | 11 | |
| 1797 | 12 | I1797V, |
| 1800 | 12 | |
| 1793 | 13 | M1793K, |
| 1848 | 14 | |
| 1817 | 14 | |
| 1796 | 10 | |
| 1799 | 8 | |
| 1788 | 14 | c.5361_5364delTGAG, |
| 1500 | 15 | p.K1500del, |
| 1791 | 12 | |
| 1852 | 14 | D1852V, |
| 1792 | 11 | D1792Y, D1792N, D1792V, |
| 1508 | 7 | |
| 1502 | 12 | G1502A, G1502S, |
| 1805 | 6 | |
| 1809 | 12 | I1809M |
| 1506 | 0 | P1506T, P1506S, |
| 1503 | 10 | S1503Y, |