SCN5A Variant c.3005-3012delCCAGCTGG
Summary of observed carriers, functional annotations, and structural context for SCN5A c.3005-3012delCCAGCTGG. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
3%
0/11 effective observations
Estimated BrS1 penetrance
34%
3/11 effective observations
Total carriers
1
1 BrS1 · 0 LQT3 · 0 unaffected
Variant features alone are equivalent to phenotyping 2 individuals for Brugada syndrome and 0 individuals for LQT3.
In silico predictors
| PROVEAN | PolyPhen-2 | BLAST-PSSM | REVEL | Penetrance Density BrS (%) | Penetrance Density LQT3 (%) |
|---|---|---|---|---|---|
| NA | NA | NA | None | 35 | 1 |
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 |
|---|---|---|---|---|---|---|---|
| 19029124 | 2009 | 1 | 0 | 1 | 0 | ||
| Literature, cohort, and gnomAD | – | 1 | 0 | 0 | 1 | – | |
| Variant features alone | – | 15 | 13 | 0 | 2 | – | – |
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) |
|---|---|---|---|---|---|---|
| 19029124 | 2009 |
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 |
|---|---|---|
| 987 | 15 | |
| 988 | 14 | R988W, R988Q, |
| 989 | 14 | |
| 990 | 13 | |
| 991 | 13 | K991E, K991T, |
| 992 | 12 | |
| 993 | 11 | A993T, A993S, |
| 994 | 11 | A994V, A994T, |
| 995 | 10 | L995F, |
| 996 | 9 | A996T, |
| 997 | 8 | A997S, A997T, A997D |
| 998 | 8 | |
| 999 | 7 | G999D, |
| 1000 | 5 | Q1000X, p.Gln1000del, Q1000L, |
| 1001 | 4 | |
| 1002 | 0 | c.3005-3012delCCAGCTGG, P1002S, |
| 1003 | 4 | |
| 1004 | 5 | C1004R, |
| 1005 | 7 | I1005V, I1005T, |
| 1006 | 8 | A1006S, |
| 1007 | 8 | T1007I, T1007N, |
| 1008 | 9 | P1008S, |
| 1009 | 10 | |
| 1010 | 11 | |
| 1011 | 11 | P1011S, P1011L, |
| 1012 | 12 | |
| 1013 | 13 | |
| 1014 | 13 | P1014S, |
| 1015 | 14 | E1015K, p.G1015DfsX14, |
| 1016 | 14 | T1016M, c.3045_3046delGA, |
| 1017 | 15 |