SCN5A Variant S1602P

Summary of observed carriers, functional annotations, and structural context for SCN5A S1602P. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

6%

0/10 effective observations

Estimated BrS1 penetrance

22%

2/10 effective observations

Total carriers

0

0 BrS1 · 0 LQT3 · 0 unaffected

S1602P has not been reported in gnomAD. This residue resides in a Mild_Hotspot region for Brugada syndrome and a Non_Hotspot region for LQT3.

Variant features alone are equivalent to phenotyping 2 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 (%)
NA NA NA 0.968 25 3

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 – 0 0 0 0 –
Variant features alone – 15 13 0 2 – –

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 S1602P.
Neighbour residue Distance (Å) Observed variants
1569 9 A1569P,
1627 14
1567 11 F1567L, F1567L, F1567L,
1624 13 V1624I,
1538 14
1566 12
1568 6
1602 0
1601 5 L1601H,
1609 11 S1609W, S1609L,
1575 11 C1575S, C1575S,
1562 15
1608 9
1613 14 Q1613L, Q1613H, Q1613H,
1600 6
1571 9 F1571C,
1572 9
1564 9
1570 12 p.I1570dup, I1570V, p.1570_F1571insI,
1599 5
1545 14
1626 9 R1626C, R1626H, R1626L, R1626P,
1603 4 I1603F,
1625 10
1606 5 T1606I,
1560 15 L1560F, L1560F,
1610 13 D1610G,
1576 14
1596 10 F1596I, F1596C,
1628 15
1597 9 V1597M,
1620 14 T1620K, T1620M,
1573 12
1537 15
1565 9 L1565M,
1594 14 F1594S,
1593 15 I1593M,
1595 11
1619 11 c.4856delC, P1619L, P1619Q,
1629 12 R1629X, R1629Q, R1629G,
1605 5 G1605C, G1605D, c.4813+2_4813+5dupTGGG, c.4813+5insTGGG, c.4813+3_4813+6dupGGGT,
1574 13 E1574K, c.4719C>T,
1563 13
1541 12
1616 12
1607 8
1617 9 p.F1617del,
1604 6 V1604M, c.4810+3_4810+6dupGGGT,
1622 7
1618 11
1621 12
1598 6 V1598A,
1561 12
1623 12 c.4867delC, R1623Q, R1623X, R1623L,