SCN5A Variant V1598A

Summary of observed carriers, functional annotations, and structural context for SCN5A V1598A. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

4%

0/11 effective observations

Estimated BrS1 penetrance

9%

0/11 effective observations

Total carriers

1

0 BrS1 · 0 LQT3 · 1 unaffected

V1598A 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 (%)
-3.62 0.982 -2.7 0.924 3 7

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 V1598A.
Neighbour residue Distance (Å) Observed variants
1569 12 A1569P,
1627 10
1586 12
1567 12 F1567L, F1567L, F1567L,
1624 9 V1624I,
1538 11
1566 14
1568 8
1587 14 F1587V,
1602 6
1534 13
1542 13
1601 6 L1601H,
1575 10 C1575S, C1575S,
1608 15
1600 6
1571 8 F1571C,
1572 10
1564 12
1570 12 p.1570_F1571insI, I1570V, p.I1570dup,
1599 4
1545 13
1630 13 I1630V, I1630R,
1626 6 R1626C, R1626H, R1626P, R1626L,
1603 9 I1603F,
1625 5
1606 12 T1606I,
1576 14
1596 7 F1596I, F1596C,
1628 9
1589 14
1632 12 R1632C, R1632H, R1632L
1539 15 C1539Y, C1539F,
1597 4 V1597M,
1620 13 T1620K, T1620M,
1573 12
1535 14
1537 13
1565 13 L1565M,
1594 8 F1594S,
1591 12 W1591X,
1593 10 I1593M,
1595 6
1619 12 P1619Q, P1619L, c.4856delC,
1629 7 R1629G, R1629X, R1629Q,
1605 11 c.4813+2_4813+5dupTGGG, c.4813+3_4813+6dupGGGT, c.4813+5insTGGG, G1605C, G1605D,
1574 10 c.4719C>T, E1574K,
1541 11
1616 15
1607 14
1592 11
1578 13 c.4732_4733dupAA,
1617 10 p.F1617del,
1631 14 G1631D,
1590 13
1604 10 c.4810+3_4810+6dupGGGT, V1604M,
1622 6
1618 12
1621 10
1579 14 L1579fsX53,
1598 0 V1598A,
1623 11 c.4867delC, R1623X, R1623Q, R1623L,