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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

L939F is present in 1 alleles in gnomAD. This residue resides in a Non_Hotspot region for Brugada syndrome and a Mild_Hotspot region for LQT3.

Variant features alone are equivalent to phenotyping 0 individuals for Brugada syndrome and 0 individuals for LQT3.

In silico predictors

Variant-level computational 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

Observed carriers by publication or cohort.
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.

Previously observed variants near L939F.
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,