SCN5A Variant G1639A
Summary of observed carriers, functional annotations, and structural context for SCN5A G1639A. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
7%
0/12 effective observations
Estimated BrS1 penetrance
9%
1/12 effective observations
Total carriers
2
0 BrS1 · 0 LQT3 · 2 unaffected
Variant features alone are equivalent to phenotyping 1 individuals for Brugada syndrome and 0 individuals for LQT3.
In silico predictors
PROVEAN | PolyPhen-2 | BLAST-PSSM | REVEL | Penetrance Density BrS (%) | Penetrance Density LQT3 (%) |
---|---|---|---|---|---|
-3.7 | 0.967 | 0.39 | 0.59 | 8 | 5 |
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 | – | 2 | 2 | 0 | 0 | – | |
Variant features alone | – | 15 | 14 | 0 | 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 |
---|---|---|
1643 | 9 | I1643L, |
1635 | 13 | |
1634 | 12 | L1634P, |
1641 | 5 | |
1639 | 0 | G1639A |
1787 | 14 | S1787N, |
1648 | 14 | |
1532 | 14 | V1532I, V1532F, |
1644 | 7 | R1644L, R1644C, R1644H, |
1640 | 3 | |
256 | 14 | |
1793 | 12 | M1793K, |
1789 | 10 | |
255 | 13 | |
1645 | 10 | T1645M, |
1796 | 15 | |
251 | 14 | |
1638 | 6 | R1638Q, R1638X, |
1633 | 12 | |
1637 | 6 | |
253 | 14 | |
1792 | 14 | D1792N, D1792V, D1792Y, |
1636 | 9 | |
1823 | 13 | E1823K, p.E1823HfsX10, |
1642 | 8 | G1642E, |
1528 | 14 | |
1790 | 13 | D1790G, D1790N, p.D1790del, |
252 | 10 | |
1647 | 12 | |
1822 | 12 | c.5464_5467delTCTG, c.5464-5467delTCTG, |
1646 | 13 | |
1782 | 14 |