SCN5A Variant T486S

Summary of observed carriers, functional annotations, and structural context for SCN5A T486S. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

2%

0/11 effective observations

Estimated BrS1 penetrance

1%

0/11 effective observations

Total carriers

1

0 BrS1 · 0 LQT3 · 1 unaffected

T486S 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 (%)
0.46 0.021 0.69 0.165 0 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 T486S.
Neighbour residue Distance (Å) Observed variants
471 15
472 14
473 14 E473X,
474 13 R474G, R474K,
475 13 R475S, R475K, R475S,
476 12
477 11 c.1428_1431delCAAG,
478 11
479 10
480 9 K480N, K480N,
481 8 R481Q, R481W,
482 8 M482I, M482I, M482I
483 7
484 5
485 4
486 0 T486S, T486S, T486A,
487 4
488 5
489 7
490 8 G490A, G490E,
491 8 E491G,
492 9
493 10 R493K,
494 11
495 11
496 12 K496N, K496M, K496N,
497 13 S497C,
498 13
499 14
500 14 E500K,
501 15 D501G,