SCN5A Variant K496N

Summary of observed carriers, functional annotations, and structural context for SCN5A K496N. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

6%

0/11 effective observations

Estimated BrS1 penetrance

5%

0/11 effective observations

Total carriers

1

0 BrS1 · 0 LQT3 · 1 unaffected

K496N is present in 1 alleles in gnomAD. This residue resides in a Non_Hotspot region for Brugada syndrome and a Non_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 (%)
-3.75 0.999 -0.67 0.449 1 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 – 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 K496N.
Neighbour residue Distance (Å) Observed variants
481 15 R481W, R481Q,
482 14 M482I, M482I, M482I,
483 14
484 13
485 13
486 12 T486S, T486A, T486S,
487 11
488 11
489 10
490 9 G490A, G490E,
491 8 E491G,
492 8
493 7 R493K,
494 5
495 4
496 0 K496N, K496N, K496M,
497 4 S497C,
498 5
499 7
500 8 E500K,
501 8 D501G,
502 9
503 10 P503S,
504 11 R504T,
505 11 A505E,
506 12 M506K,
507 13 p.N507_L515dup,
508 13
509 14
510 14
511 15