SCN5A Variant p.L1716SfsX71

Summary of observed carriers, functional annotations, and structural context for SCN5A p.L1716SfsX71. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

3%

0/11 effective observations

Estimated BrS1 penetrance

23%

2/11 effective observations

Total carriers

1

0 BrS1 · 0 LQT3 · 1 unaffected

p.L1716SfsX71 is present in 1 alleles in gnomAD. This residue resides in a Mild_Hotspot region for Brugada syndrome and a Non_Hotspot region for LQT3.

Variant features alone are equivalent to phenotyping 2 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 (%)
NA NA NA None 32 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

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 13 0 2 – –

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 p.L1716SfsX71.
Neighbour residue Distance (Å) Observed variants
1702 12
1746 15 A1746T, A1746V,
1417 14
1715 4
1687 6
1413 14
1698 15 A1698T,
1745 14
1756 12 I1756V
1675 12
1743 13 G1743R, G1743R, G1743E,
1711 8 c.5131delG,
1754 15
1707 7
1694 9
1704 10 L1704H,
1410 14
1706 8 Q1706H, Q1706H,
1747 13 V1747M,
1716 0 p.L1716SfsX71,
1695 14 Q1695X,
376 13 R376C, R376H,
1714 7 D1714G,
1688 7
1684 12 W1684R, W1684R,
1671 14
1423 15 D1423H,
1668 14 M1668T,
1676 14 M1676T, M1676I, M1676I, M1676I,
1692 9
1744 12 S1744I,
1721 10
1753 13 T1753A,
1672 14 S1672Y,
1693 10
378 13
1699 12
373 14
1712 5 G1712S, G1712C,
379 11
1680 14 A1680T, A1680P,
1703 7
1719 6
1709 12 p.T1709del, T1709R, T1709M,
1701 14 M1701I, M1701I, M1701I,
1420 12 G1420R, G1420D, G1420V, G1420P,
1690 13 c.5068_5070delGA, D1690N,
1678 14 N1678S,
1755 12
1399 13
1713 7
1748 10 p.G1748del, G1748D,
1708 12 T1708I,
1683 13
1400 14 V1400I,
1718 7 S1718R, S1718R, S1718R,
374 13 W374G,
1705 13
1689 11 D1689N,
1700 11
1717 5 L1717P,
1751 10
1682 11
1750 15 L1750F,
1752 7
1722 14 N1722D,
1686 7
1749 12 I1749N,
375 9
1691 13
1710 11 S1710L,
1720 7 c.5157delC,
1679 10
1685 9
1419 11 K1419E,
1414 11 Q1414H, Q1414H,