SCN5A Variant T1544P
Summary of observed carriers, functional annotations, and structural context for SCN5A T1544P. Data combine curated literature, international cohorts, and gnomAD observations.
Estimated LQT3 penetrance
48%
2/11 effective observations
Estimated BrS1 penetrance
11%
1/11 effective observations
Total carriers
1
0 BrS1 · 1 LQT3 · 0 unaffected
Variant features alone are equivalent to phenotyping 1 individuals for Brugada syndrome and 1 individuals for LQT3.
In silico predictors
| PROVEAN | PolyPhen-2 | BLAST-PSSM | REVEL | Penetrance Density BrS (%) | Penetrance Density LQT3 (%) |
|---|---|---|---|---|---|
| -5.48 | 0.996 | -3.81 | 0.959 | 4 | 52 |
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 |
|---|---|---|---|---|---|---|---|
| 23631430 | 2013 | 1 | 1 | 0 | 0 | ||
| Literature, cohort, and gnomAD | – | 1 | 0 | 1 | 0 | – | |
| Variant features alone | – | 15 | 13 | 1 | 1 | – | – |
Totals may differ from individual publications due to duplicate patients removed during curation.
Functional data
Peak and late/persistent current values are relative to wild-type (100% indicates no change). V1/2 activation and inactivation denote the membrane potentials (mV) at which half-maximal current is achieved.
| PubMed ID | Year | Cell Type | Peak Current (% WT) | V1/2 Activation (mV) | V1/2 Inactivation (mV) | Late/Persistent Current (% WT) |
|---|---|---|---|---|---|---|
| 23631430 | 2013 |
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 |
|---|---|---|
| 266 | 10 | L266H, |
| 1544 | 0 | T1544P, |
| 270 | 10 | Q270K, |
| 1627 | 11 | |
| 1567 | 8 | F1567L, F1567L, F1567L, |
| 1624 | 15 | V1624I, |
| 1536 | 12 | |
| 1552 | 14 | Q1552R, Q1552L, |
| 1549 | 12 | |
| 1538 | 10 | |
| 1566 | 11 | |
| 1556 | 10 | |
| 1568 | 13 | |
| 1543 | 4 | V1543L, V1543L, V1543A, |
| 1558 | 13 | |
| 1534 | 15 | |
| 1542 | 7 | |
| 1557 | 12 | I1557V, |
| 1562 | 12 | |
| 1571 | 13 | F1571C, |
| 1564 | 7 | |
| 1570 | 14 | p.1570_F1571insI, I1570V, p.I1570dup, |
| 1546 | 7 | M1546T, |
| 1545 | 5 | |
| 1630 | 13 | I1630V, I1630R |
| 1626 | 10 | R1626C, R1626H, R1626P, R1626L, |
| 267 | 14 | |
| 1560 | 6 | L1560F, L1560F, |
| 262 | 13 | S262G, |
| 357 | 14 | |
| 273 | 14 | |
| 1559 | 9 | I1559V, |
| 1628 | 15 | |
| 1553 | 14 | S1553R, S1553R, S1553R, |
| 1539 | 10 | C1539Y, C1539F, |
| 269 | 11 | |
| 1535 | 15 | |
| 1537 | 10 | |
| 1565 | 12 | L1565M, |
| 1548 | 7 | E1548K, G1548K, |
| 1555 | 15 | E1555K, |
| 265 | 14 | A265V, |
| 358 | 11 | |
| 263 | 13 | V263I, |
| 1629 | 14 | R1629G, R1629X, R1629Q, |
| 1547 | 6 | V1547L, V1547L, |
| 1563 | 6 | |
| 1541 | 5 | |
| 1540 | 7 | |
| 268 | 15 | G268S, |
| 1622 | 14 | |
| 1561 | 10 | |
| 1623 | 12 | c.4867delC, R1623X, R1623Q, R1623L, |