SCN5A Variant c.4389_4396delCCTCTTTA
Summary of observed carriers, functional annotations, and structural context for SCN5A c.4389_4396delCCTCTTTA. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
5%
0/11 effective observations
Estimated BrS1 penetrance
42%
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 0 individuals for LQT3.
In silico predictors
| PROVEAN | PolyPhen-2 | BLAST-PSSM | REVEL | Penetrance Density BrS (%) | Penetrance Density LQT3 (%) |
|---|---|---|---|---|---|
| NA | NA | NA | None | 50 | 4 |
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 |
|---|---|---|---|---|---|---|---|
| 28341781 | 2017 | 1 | 0 | 1 | 0 | ||
| 20129283 | 2010 | 1 | 0 | 1 | 0 | ||
| Literature, cohort, and gnomAD | – | 1 | 0 | 0 | 1 | – | |
| Variant features alone | – | 15 | 12 | 0 | 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 |
|---|---|---|
| 939 | 9 | L939F, |
| 937 | 11 | |
| 1417 | 15 | |
| 1765 | 11 | |
| 839 | 13 | L839P, |
| 943 | 12 | S943N, |
| 1340 | 9 | V1340I, |
| 1457 | 9 | |
| 1453 | 14 | |
| 1455 | 13 | |
| 1757 | 13 | |
| 1472 | 12 | N1472S, p.N1472del, |
| 1339 | 12 | p.L1339del, L1339F, |
| 1461 | 5 | T1461S, T1461S, |
| 1764 | 14 | c.5290delG, V1764F, |
| 409 | 14 | L409V, L409P, |
| 1333 | 10 | |
| 1344 | 11 | F1344S, F1344L, F1344L, F1344L, |
| 825 | 13 | |
| 934 | 9 | |
| 1458 | 10 | S1458Y, |
| 933 | 14 | |
| 1471 | 11 | |
| 935 | 9 | L935P, |
| 1762 | 12 | I1762M, p.I1762del, |
| 1470 | 10 | |
| 1464 | 0 | L1464P, c.4389_4396delCCTCTTTA, |
| 1466 | 7 | c.4396_4397insG, |
| 944 | 12 | |
| 1769 | 14 | |
| 1766 | 14 | M1766L, M1766T, M1766L, M1766V, |
| 1768 | 13 | I1768V, |
| 940 | 12 | S940N, |
| 1334 | 10 | I1334V, |
| 1341 | 8 | |
| 1468 | 7 | V1468A, V1468F, |
| 831 | 11 | |
| 1462 | 7 | |
| 938 | 6 | |
| 942 | 7 | |
| 1456 | 11 | |
| 1459 | 11 | c.4376_4379delTCTT, |
| 1330 | 13 | A1330D, A1330P, A1330T, |
| 827 | 13 | |
| 1460 | 6 | F1460L, F1460L, F1460L, |
| 1454 | 14 | |
| 1338 | 10 | L1338V, |
| 1343 | 14 | |
| 1345 | 12 | W1345C, W1345C, |
| 941 | 10 | S941F, S941N, |
| 1337 | 7 | |
| 1342 | 14 | |
| 936 | 11 | |
| 1416 | 13 | A1416E, c.4245+1G>C, A1416G, c.4245+2T>A, c.4245+1G>A, |
| 1332 | 14 | P1332Q, P1332L, |
| 1465 | 5 | p.F1465_L1480dup, |
| 1760 | 13 | |
| 1467 | 6 | |
| 1331 | 14 | I1331V, |
| 1761 | 10 | L1761H, L1761F, c.5280delG, |
| 1469 | 9 | I1469V, |
| 1336 | 11 | |
| 824 | 13 | |
| 829 | 13 | |
| 932 | 13 | |
| 1335 | 13 | M1335R, |
| 832 | 11 | |
| 835 | 13 | S835L, S835A, |
| 828 | 9 | L828V, |
| 931 | 13 | |
| 1463 | 5 | N1463Y, |