SCN5A Variant A413P

Summary of observed carriers, functional annotations, and structural context for SCN5A A413P. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

41%

2/10 effective observations

Estimated BrS1 penetrance

14%

1/10 effective observations

Total carriers

0

0 BrS1 · 0 LQT3 · 0 unaffected

A413P has not been reported in gnomAD. This residue resides in a Non_Hotspot region for Brugada syndrome and a Hotspot region for LQT3.

Variant features alone are equivalent to phenotyping 1 individuals for Brugada syndrome and 2 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 0.901 10 54

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 12 2 1 – –

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 A413P.
Neighbour residue Distance (Å) Observed variants
414 5 M414V,
939 8 L939F,
404 15 L404V, L404Q,
937 10
1778 13
1773 11
842 14
249 10 K249X,
943 14 S943N,
247 13 V247L, V247L,
240 15 V240M,
1771 12 I1771T,
1777 13 V1777M, V1777L, V1777L,
418 9 E418K,
926 15
250 12
409 6 L409V, L409P,
928 12 L928P,
417 6
934 11
933 7
1471 13
246 8
935 8 L935P,
1779 11 T1779M,
412 4 V412D,
1470 11
927 14 N927S, N927K, N927K,
1466 12 c.4396_4397insG,
245 11 Q245K,
1776 9
244 14
1769 12
415 5 A415T,
1768 12 I1768V,
940 9 S940N,
1774 13 N1774D, c.5321_5324dupACTT,
405 13
420 10
248 15
1474 14
938 11
241 12
942 14
419 11 Q419X,
930 12 c.2787+17_2787+18insACACACACACACACACACACACA, c.2788-6C>T,
1772 8 L1772V,
239 12 I239V, I239V ,
410 5 A410V,
1780 12 E1780G
242 9 A242D,
1770 15 I1770V,
929 10
416 6 Y416C,
413 0 A413T, A413E,
408 9
253 14
941 13 S941N, S941F,
407 10
936 5
238 13
838 15
422 14
1467 12
1775 9 F1775V, p.F1775LfsX15,
421 12
406 11 N406S, N406K, N406K,
411 6 V411M,
243 11
932 8
931 12
1646 14
1463 14 N1463Y,