SCN5A Variant S497A

Summary of observed carriers, functional annotations, and structural context for SCN5A S497A. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

3%

0/10 effective observations

Estimated BrS1 penetrance

8%

0/10 effective observations

Total carriers

0

0 BrS1 · 0 LQT3 · 0 unaffected

S497A has not been reported 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 (%)
NA NA NA 0.533 3 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 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 S497A.
Neighbour residue Distance (Å) Observed variants
482 15 M482I, M482I, M482I,
483 14
484 14
485 13
486 13 T486A, T486S, T486S,
487 12
488 11
489 11
490 10 G490E, G490A,
491 9 E491G,
492 8
493 8 R493K,
494 7
495 5
496 4 K496M, K496N, K496N,
497 0 S497C,
498 4
499 5
500 7 E500K,
501 8 D501G,
502 8
503 9 P503S,
504 10 R504T,
505 11 A505E,
506 11 M506K,
507 12 p.N507_L515dup,
508 13
509 13
510 14
511 14
512 15 T512I