We estimate the penetrance of LQTS for SCN5A E1225K around 7% and the Brugada syndrome penetrance around 66%. SCN5A E1225K was found in a total of 14 carriers in 17 papers and/or in gnomAD: 11 had Brugada syndrome, 1 had LQTS. E1225K is present in 1 alleles in gnomAD. E1225K has been functionally characterized in 18 papers. This residue is located in a Hotspot region for Brugada syndrome and a Non_Hotspot region for LQTS. In silico predictions, functional data (if available), and location in structure are equivalent to phenotyping 10 individuals for Brugada syndrome (4 diagnosed with Brugada syndrome) and 5 individuals for LQTS (0 with LQTS). These data combined with observations of carriers lead us to estimate the LQTS penetrance for SCN5A E1225K around 7% (1/24) and the Brugada syndrome penetrance around 66% (15/24).

PROVEAN	PolyPhen-2	BLAST-PSSM	REVEL	Penetrance Density BrS (%)	Penetrance Density LQT3 (%)
-3.91	1	-2.67	0.95	72	8

PROVEAN scores less than -2 are considered deleterious. REVEL scores higher than 0.5 or 0.75 are considered likely pathogenic (higher sensitivity with the former cutoff, higher specificity with the latter cutoff). A PolyPhen-2 score of 0.85 or greater is considered likely pathogenic. BLAST-PSSM reflects the evolutionary conservation of residue substitutions, more negative numbers indicate fewer observations of the specific substitution than is expected. Penetrance Density is our previously published method to calculate the average BrS/LQTS probability density in a shell of residues surrounding a residue of interest (Kroncke et al. 2019).

PubMed ID	Year	Carriers	Unaffected	LQT3	BrS1	Other	Other Disease
12106943	2002	1		0	1	0
14961552	2003	3		0	2	0
15840476	2005	1		1	0	0
17404158	2007	1		0	1	0
22840528	2012	2		0	2	0
23321620	2013	1		0	1	0
24721456	2014	1		0	1	0
26921764	2016	1		0	1	0
26941339	2016	1		0	1	0
28341781	2017	2		0	2	0
28781330	2017	1		0	1	0
20129283	2010	1		0	1	0
20129283	2010	1		0	1	0
20129283	2010	1		0	1	0
20129283	2010	1		0	1	0
29574140	2018	2		0	2	0
30059973	2018	3		3	0	0
LITERATURE, COHORT, AND GNOMAD:	-	14	2	1	11		-
VARIANT FEATURES ALONE:	-	15	11	0	4	-	-

Summary totals might not agree with the literature table because of duplicate patients, which were excluded from the total counts. We do not distinguish here between multiple missense codons. Missense variants are combined across degenerate codon substitutions since codon-level data were not consistently available for curation.

Peak and late/persistent current are relative to wildtype (100% being no different from wildtype). V_0.5 act/inact are the voltages at which half of the maximal current is reached during an activation and inactivation protocol, each is in units of mV and relative to wildtype.

PubMed ID	Year	Cell Type	Peak Current (%WT)	V1/2 Act. (mV)	V1/2 Inact. (mV)	Late/Persistent Current (%WT)
29574140	2018
30059973	2018
32533946	2020	HEK	36	3.9	11.5
12106943	2002
14961552	2003
15840476	2005
17404158	2007
22840528	2012
23321620	2013
24721456	2014
26921764	2016
26941339	2016
28341781	2017
28781330	2017
20129283	2010
20129283	2010
20129283	2010
20129283	2010

A residue within a folded protein on average has nearest neighbors that fall roughly into two shells: a "nearest" neighbor around 5-6 angstroms and a second shell around 11 angstroms. All variants shown in the rightmost column have been observed in at least one individual in the literature or gnomAD.

Neighbor	Distance (Angstroms)	Variants Observed in Individuals
1233	12	K1233E,
1218	11	S1218I, S1218T,
1304	10	T1304M,
1217	14
1243	11	D1243N,
1234	11
1698	14	A1698T,
1285	15
1299	13	c.3894delC,
1220	10	G1220E,
1673	8
1675	12
1681	13	c.5040_5042delTTAinsC, Y1681F,
1694	14
1241	14
1226	4
1695	12	Q1695X,
1669	12
1221	7	A1221V,
1242	11
1676	8	M1676T, M1676I,
1219	10	S1219N,
1672	11	S1672Y,
1699	15
1239	6	L1239P,
1306	12	R1306S, R1306H,
1305	14
1680	12	A1680P, A1680T,
1246	14
1235	7
1302	13	p.L1302Vfs18,
1231	12	E1231K,
1237	11	V1237F,
1307	13
1228	9	Y1228F, Y1228H, Y1228C,
1678	13	N1678S,
1223	7	c.3667delG,
1697	10
1222	6	p.L1222LfsX7, L1222R,
1230	10	E1230K,
1227	8
1300	13
1674	13	F1674V,
1229	6
1301	9
1696	10
1700	13
1677	9
1224	7
1670	14
1240	9	E1240Q,
1225	0	E1225K, G1225K,
1232	15	R1232W, R1232Q,
1238	11
1679	14
1236	8	K1236R, K1236N,
1303	8	R1303Q, R1303W,