SCN5A Variant T1147N

Summary of observed carriers, functional annotations, and structural context for SCN5A T1147N. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

0/28 effective observations

Estimated BrS1 penetrance

0/28 effective observations

Total carriers

0 BrS1 · 0 LQT3 · 18 unaffected

T1147N is present in 18 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 (%)
-1.09	0.034	-0.15	0.347	0	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	–	18	18	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 T1147N.
Neighbour residue	Distance (Å)	Observed variants
1132	15	P1132S,
1133	14
1134	14	D1134N, D1134E, D1134E,
1135	13	S1135I
1136	13	C1136Y,
1137	12
1138	11
1139	11
1140	10	S1140T,
1141	9
1142	8
1143	8
1144	7
1145	5
1146	4
1147	0	T1147I, T1147N, T1147S, T1147S,
1148	4	A1148S, A1148T,
1149	5
1150	7
1151	8
1152	8	E1152X,
1153	9	Q1153H, Q1153H,
1154	10	I1154N,
1155	11	P1155S,
1156	11	D1156G,
1157	12
1158	13	G1158S,
1159	13
1160	14
1161	14	c.3480delT,
1162	15