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SCN5A Variant T531A

Summary of observed carriers, functional annotations, and structural context for SCN5A T531A. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

6%

0/12 effective observations

Estimated BrS1 penetrance

6%

0/12 effective observations

Total carriers

2

0 BrS1 · 0 LQT3 · 2 unaffected

T531A is present in 2 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 (%)
-1.01 0.983 0.57 0.538 3 6

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 2 2 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 T531A.
Neighbour residue Distance (Å) Observed variants
516 15
517 14 R517S,
518 14
519 13 S519F,
520 13 M520R, M520V
521 12 K521E, c.1562delA,
522 11 P522S,
523 11 R523H, R523S, R523C,
524 10 c.1570_1571insG, S524Y,
525 9 S525G,
526 8 R526H, R526C,
527 8 G527R,
528 7 S528R,
529 5
530 4 F530V, F530S,
531 0 T531I, T531A,
532 4 F532C, F532L,
533 5 R533S, R533H, R533C,
534 7
535 8 R535Q, R535G, R535X,
536 8 D536H,
537 9
538 10 G538D,
539 11
540 11
541 12
542 13
543 13 F543L,
544 14
545 14
546 15