SCN5A Variant A467D

Summary of observed carriers, functional annotations, and structural context for SCN5A A467D. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

0/10 effective observations

Estimated BrS1 penetrance

11%

1/10 effective observations

Total carriers

0 BrS1 · 0 LQT3 · 0 unaffected

A467D has not been reported 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 1 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	0.535	8	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	14	0	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 A467D.
Neighbour residue	Distance (Å)	Observed variants
452	15	G452D,
453	14	V453M,
454	14
455	13
456	13	V456M,
457	12
458	11	R458C, R458H, p.R458VfsX12,
459	11	S459G,
460	10
461	9	L461V,
462	8	E462K, E462A,
463	8	M463R, M463T,
464	7
465	5	p.P465LfsX5,
466	4	L466F,
467	0
468	4	P468L,
469	5	V469I,
470	7	N470K,
471	8
472	8
473	9	E473X,
474	10	R474G, R474K,
475	11	R475K, R475S,
476	11
477	12	c.1428_1431delCAAG,
478	13
479	13
480	14	K480N,
481	14	R481Q, R481W,
482	15	M482I,