SCN5A Variant c.3667delG
Summary of observed carriers, functional annotations, and structural context for SCN5A c.3667delG. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
10%
1/15 effective observations
Estimated BrS1 penetrance
41%
6/15 effective observations
Total carriers
5
3 BrS1 · 0 LQT3 · 2 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 (%) |
|---|---|---|---|---|---|
| NA | NA | NA | None | 41 | 25 |
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 |
|---|---|---|---|---|---|---|---|
| 17404158 | 2007 | 1 | 0 | 1 | 0 | ||
| 20031634 | 2009 | 5 | 0 | 3 | 0 | ||
| 26921764 | 2016 | 1 | 0 | 1 | 0 | ||
| 20129283 | 2010 | 1 | 0 | 1 | 0 | ||
| Literature, cohort, and gnomAD | – | 5 | 2 | 0 | 3 | – | |
| 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.
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 |
|---|---|---|
| 1702 | 14 | |
| 387 | 15 | |
| 1218 | 9 | S1218T, S1218I, |
| 1304 | 11 | T1304M, |
| 1217 | 11 | |
| 1243 | 15 | D1243N, |
| 1216 | 11 | L1216V, |
| 1234 | 15 | |
| 1698 | 9 | A1698T, |
| 1220 | 5 | G1220E, |
| 1673 | 7 | |
| 1675 | 12 | |
| 1694 | 13 | |
| 1704 | 14 | L1704H |
| 1226 | 7 | |
| 1695 | 13 | Q1695X, |
| 1669 | 7 | |
| 1671 | 14 | |
| 1221 | 5 | A1221V, |
| 1668 | 12 | M1668T, |
| 1242 | 13 | |
| 1676 | 8 | M1676T, M1676I, M1676I, M1676I, |
| 1219 | 7 | S1219N, |
| 1672 | 8 | S1672Y, |
| 1699 | 12 | |
| 1693 | 14 | |
| 1239 | 10 | L1239P, |
| 1310 | 13 | |
| 1306 | 12 | R1306S, R1306H, |
| 1665 | 12 | |
| 1305 | 15 | |
| 1680 | 15 | A1680T, A1680P, |
| 1246 | 15 | |
| 1235 | 10 | |
| 1231 | 15 | E1231K, |
| 1701 | 10 | M1701I, M1701I, M1701I, |
| 1307 | 10 | |
| 1228 | 10 | Y1228H, Y1228C, Y1228F, |
| 1678 | 15 | N1678S, |
| 1223 | 0 | c.3667delG, |
| 1697 | 6 | |
| 1222 | 5 | p.L1222LfsX7, L1222R, |
| 1227 | 11 | |
| 1674 | 13 | F1674V, |
| 1229 | 11 | |
| 1215 | 13 | I1215V, |
| 1301 | 13 | |
| 1696 | 8 | |
| 1700 | 10 | |
| 1677 | 12 | |
| 1308 | 14 | L1308F, |
| 1224 | 4 | |
| 1670 | 11 | |
| 1240 | 14 | E1240Q, |
| 1225 | 7 | E1225K, G1225K, |
| 1238 | 13 | |
| 1679 | 15 | |
| 1236 | 14 | K1236R, K1236N, K1236N, |
| 1667 | 14 | V1667I, |
| 1303 | 11 | R1303W, R1303Q, |
| 1666 | 12 |