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
Variant features alone are equivalent to phenotyping 0 individuals for Brugada syndrome and 0 individuals for LQT3.
In silico 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
| 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.
| 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 |