SCN5A Variant L939F
Summary of observed carriers, functional annotations, and structural context for SCN5A L939F. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
11%
0/11 effective observations
Estimated BrS1 penetrance
8%
0/11 effective observations
Total carriers
1
0 BrS1 · 0 LQT3 · 1 unaffected
Variant features alone are equivalent to phenotyping 0 individuals for Brugada syndrome and 0 individuals for LQT3.
In silico predictors
PROVEAN | PolyPhen-2 | BLAST-PSSM | REVEL | Penetrance Density BrS (%) | Penetrance Density LQT3 (%) |
---|---|---|---|---|---|
-3.68 | 0.999 | -0.72 | 0.872 | 3 | 16 |
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 | – | 1 | 1 | 0 | 0 | – | |
Variant features alone | – | 15 | 15 | 0 | 0 | – | – |
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 |
---|---|---|
414 | 12 | M414V, |
939 | 0 | L939F, |
937 | 7 | |
1773 | 11 | |
1765 | 13 | |
839 | 13 | L839P, |
842 | 14 | |
943 | 7 | S943N, |
1472 | 12 | N1472S, p.N1472del, |
1771 | 14 | I1771T, |
1461 | 13 | T1461S, |
418 | 14 | E418K, |
409 | 10 | L409V, L409P, |
1333 | 15 | |
417 | 9 | |
934 | 9 | |
933 | 10 | |
1471 | 7 | |
935 | 7 | L935P, |
412 | 11 | V412D, |
1470 | 7 | |
1464 | 9 | L1464P, c.4389_4396delCCTCTTTA, |
1466 | 8 | c.4396_4397insG, |
1776 | 12 | |
944 | 10 | |
1769 | 11 | |
415 | 12 | A415T, |
1768 | 12 | I1768V, |
940 | 5 | S940N, |
1473 | 13 | F1473C, F1473S, |
1468 | 9 | V1468A, V1468F, |
831 | 12 | |
1462 | 14 | |
420 | 11 | |
1474 | 11 | |
938 | 5 | |
942 | 7 | |
419 | 15 | Q419X, |
930 | 14 | c.2787+17_2787+18insACACACACACACACACACACACA, c.2788-6C>T, |
1459 | 15 | c.4376_4379delTCTT, |
834 | 15 | N834D, |
1772 | 10 | L1772V, |
1460 | 12 | F1460L, |
239 | 15 | I239V, I239V , |
410 | 11 | A410V, |
242 | 15 | A242D, |
1770 | 15 | I1770V, |
416 | 9 | Y416C, |
413 | 8 | A413E, A413T, |
941 | 7 | S941N, S941F, |
1337 | 15 | |
936 | 5 | |
238 | 15 | |
838 | 13 | |
1465 | 12 | p.F1465_L1480dup, |
1467 | 6 | |
1775 | 14 | p.F1775LfsX15, F1775V, |
421 | 13 | |
1475 | 14 | p.Q1475NfsX6, Q1475L, |
1469 | 10 | I1469V, |
406 | 14 | N406S, N406K, |
411 | 13 | V411M, |
932 | 11 | |
832 | 14 | |
835 | 13 | S835A, S835L, |
828 | 14 | L828V, |
931 | 13 | |
1463 | 10 | N1463Y, |