SCN5A Variant N1699Y

Summary of observed carriers, functional annotations, and structural context for SCN5A N1699Y. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

4%

0/10 effective observations

Estimated BrS1 penetrance

21%

2/10 effective observations

Total carriers

0

0 BrS1 · 0 LQT3 · 0 unaffected

N1699Y has not been reported 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 0.964 23 0

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 – 0 0 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 N1699Y.
Neighbour residue Distance (Å) Observed variants
333 10 c.998+5G>A, c.998+1G>A,
1702 5
387 8
385 14 A385T,
1687 12
391 15
330 11 S330F,
388 12 I388S,
1698 4 A1698T,
1673 13
1675 12
334 13 c.999-424_1338+81del,
332 11 A332T,
1707 13
1681 13 c.5040_5042delTTAinsC, Y1681F,
1694 7
1704 9 L1704H,
1226 11
1706 11 Q1706H, Q1706H,
1695 7 Q1695X,
1716 12 p.L1716SfsX71,
384 15 S384T,
1688 10
1684 13 W1684R, W1684R,
1669 13
1671 15
329 14
1668 12 M1668T,
1676 9 M1676I, M1676I, M1676T, M1676I,
1692 6
386 11 G386R, G386R, G386E,
1672 10 S1672Y,
1693 5
378 11
1699 0
331 8
1665 15
379 11
1680 12 A1680T, A1680P,
1703 6
1719 15
1701 7 M1701I, M1701I, M1701I,
1228 11 Y1228H, Y1228C, Y1228F,
1690 9 D1690N, c.5068_5070delGA,
1223 12 c.3667delG,
1697 7
389 14 Y389X, Y389H,
1227 11
393 15
390 10
383 12
1708 15 T1708I,
382 10
1696 5
1705 10
1689 10 D1689N,
1700 5
1677 14
1682 13
1224 12
381 14 c.1140+1G>A, c.1141-3C>A,
1225 15 E1225K, G1225K,
375 14
1691 6
1679 12