SCN5A Variant p.D1790del
Summary of observed carriers, functional annotations, and structural context for SCN5A p.D1790del. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
52%
3/11 effective observations
Estimated BrS1 penetrance
8%
0/11 effective observations
Total carriers
1
0 BrS1 · 1 LQT3 · 0 unaffected
Variant features alone are equivalent to phenotyping 0 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 | None | 2 | 56 |
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 |
|---|---|---|---|---|---|---|---|
| 26496715 | 2016 | 1 | 1 | 0 | 0 | ||
| Literature, cohort, and gnomAD | – | 1 | 0 | 1 | 0 | – | |
| Variant features alone | – | 15 | 13 | 2 | 0 | – | – |
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) |
|---|---|---|---|---|---|---|
| 26496715 | 2016 |
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 | 15 | C1850S, C1850S, |
| 1855 | 15 | |
| 1785 | 9 | |
| 1794 | 8 | |
| 1856 | 14 | |
| 1778 | 12 | |
| 1853 | 14 | I1853V, |
| 1795 | 10 | Y1795N, Y1795H, p.Y1795_E1796insD, Y1795C, |
| 1818 | 13 | |
| 1652 | 15 | M1652T, M1652R, |
| 1777 | 15 | V1777M, V1777L, V1777L, |
| 1824 | 7 | P1824A, |
| 1820 | 12 | A1820T, A1820V, |
| 1504 | 11 | K1504E, |
| 1641 | 9 | |
| 1501 | 11 | p.L1501_K1505del, L1501V, |
| 1860 | 14 | c.5577_5578dupAA, |
| 1857 | 12 | |
| 1862 | 13 | |
| 1639 | 13 | G1639A, |
| 1779 | 14 | T1779M, |
| 1493 | 14 | p.K1493del, K1493X, K1493R, |
| 1858 | 10 | |
| 1865 | 14 | |
| 1787 | 4 | S1787N, |
| 1786 | 5 | c.5356_5357delCT, L1786Q, L1786R, |
| 1648 | 11 | |
| 1861 | 10 | V1861I, V1861F |
| 1649 | 14 | A1649V, |
| 1864 | 14 | |
| 1821 | 9 | |
| 1644 | 10 | R1644C, R1644H, R1644L, |
| 1640 | 14 | |
| 1798 | 14 | W1798X, |
| 1826 | 11 | R1826C, R1826H, |
| 1496 | 13 | |
| 1854 | 11 | |
| 1825 | 7 | L1825P, |
| 1797 | 11 | I1797V, |
| 1793 | 6 | M1793K, |
| 1781 | 10 | E1781G, E1781D, E1781D, |
| 1789 | 4 | |
| 1817 | 13 | |
| 1645 | 10 | T1645M, |
| 1784 | 13 | E1784K, E1784X, |
| 1827 | 14 | |
| 1498 | 14 | M1498V, M1498T, M1498R, |
| 1796 | 10 | |
| 1780 | 15 | E1780G, |
| 1788 | 7 | c.5361_5364delTGAG, |
| 1638 | 11 | R1638X, R1638Q, |
| 1500 | 9 | p.K1500del, |
| 1791 | 5 | |
| 1637 | 14 | |
| 1792 | 7 | D1792N, D1792Y, D1792V, |
| 1823 | 9 | E1823K, p.E1823HfsX10, |
| 1502 | 15 | G1502S, G1502A, |
| 1783 | 12 | |
| 1642 | 13 | G1642E, |
| 1497 | 11 | |
| 1790 | 0 | D1790N, D1790G, p.D1790del, |
| 1647 | 15 | |
| 1503 | 14 | S1503Y, |
| 1822 | 7 | c.5464_5467delTCTG, c.5464-5467delTCTG, |
| 1646 | 15 | |
| 1782 | 10 |