SCN5A Variant G490E

Summary of observed carriers, functional annotations, and structural context for SCN5A G490E. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

4%

0/11 effective observations

Estimated BrS1 penetrance

2%

0/11 effective observations

Total carriers

1

0 BrS1 · 0 LQT3 · 1 unaffected

G490E 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 (%)
0.17 0.788 0.93 0.226 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 G490E.
Neighbour residue Distance (Å) Observed variants
475 15 R475K, R475S, R475S,
476 14
477 14 c.1428_1431delCAAG,
478 13
479 13
480 12 K480N, K480N,
481 11 R481W, R481Q,
482 11 M482I, M482I, M482I,
483 10
484 9
485 8
486 8 T486A, T486S, T486S,
487 7
488 5
489 4
490 0 G490E, G490A,
491 4 E491G,
492 5
493 7 R493K,
494 8
495 8
496 9 K496M, K496N, K496N,
497 10 S497C,
498 11
499 11
500 12 E500K,
501 13 D501G,
502 13
503 14 P503S,
504 14 R504T,
505 15 A505E