SCN5A Variant R479T

Summary of observed carriers, functional annotations, and structural context for SCN5A R479T. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

0/10 effective observations

Estimated BrS1 penetrance

14%

1/10 effective observations

Total carriers

0 BrS1 · 0 LQT3 · 0 unaffected

R479T 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 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	0.186	16	0

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 R479T.
Neighbour residue	Distance (Å)	Observed variants
464	15
465	14	p.P465LfsX5,
466	14	L466F, L466F,
467	13
468	13	P468L,
469	12	V469I,
470	11	N470K, N470K,
471	11
472	10
473	9	E473X,
474	8	R474G, R474K,
475	8	R475K, R475S, R475S,
476	7
477	5	c.1428_1431delCAAG,
478	4
479	0
480	4	K480N, K480N,
481	5	R481W, R481Q,
482	7	M482I, M482I, M482I,
483	8
484	8
485	9
486	10	T486A, T486S, T486S,
487	11
488	11
489	12
490	13	G490E, G490A,
491	13	E491G,
492	14
493	14	R493K
494	15