We estimate the penetrance of LQTS for SCN5A S216L around 2% and the Brugada syndrome penetrance around 1%. SCN5A S216L was found in a total of 190 carriers in 11 papers and/or in gnomAD: 1 had Brugada syndrome, 4 had LQTS. S216L is present in 181 alleles in gnomAD. S216L has been functionally characterized in 15 papers. This residue is located in a Mild_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 (1 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 S216L around 2% (4/200) and the Brugada syndrome penetrance around 1% (2/200).

PROVEAN	PolyPhen-2	BLAST-PSSM	REVEL	Penetrance Density BrS (%)	Penetrance Density LQT3 (%)
-5.84	0.982	-3.76	0.958	9	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
21705349	2011	1		0	1	0
17210841	2007	1		0	0	1	SIDS
27287068	2016	3		3	0	0
19412328	2008	1		0	0	1	DCM
22677073	2012	1		0	0	1	SUDS
23321620	2013	1		0	1	0
24667783	2015	1		1	0	0
25163546	2015	1		0	0	1	DCM
22685113	2012	2		0	0	2	AF
20129283	2010	4		0	0	0
29672598	2018	1		0	0	1	SUDS
LITERATURE, COHORT, AND GNOMAD:	-	190	185	4	1		-
VARIANT FEATURES ALONE:	-	15	14	0	1	-	-

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)
29017927	2017
23465283	2013
17646591	2007
22685113	2012	HEK
20129283	2010
19412328	2008
29672598	2018
17210841	2007	tsA205	100	-0.2	4.7	777
27287068	2016	Oocytes	130
21705349	2011	HEK-tSA201	40	1	1	83
22378279	2012
22677073	2012
23321620	2013
24667783	2015
25163546	2015

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
223	13	V223L,
856	11	V856L,
862	11
867	14	E867K, E867X, E867Q,
859	7
209	14	N209T, N209S,
863	10
156	15	W156R, W156X,
864	12
216	0	S216L, S216X,
221	9
222	10	R222Q, R222L, R222X,
224	14	L224F,
213	8
857	11	G857D,
881	15
860	8	p.L860fsx89,
206	11
214	7
858	12	M858L,
211	11
217	4
855	13
913	14
148	15
210	13	I210T,
204	12	c.611+1G>A, A204V, A204T, c.611+3_611+4dupAA,
910	13	S910L,
203	10
208	14	E208K,
202	15	I202T,
161	15	E161Q, E161K,
219	6	c.656_657insATTCA, R219C, R219H, p.R219HfsX11,
151	14
218	6
207	9
212	8	L212Q, L212P,
215	4	p.L215CfsX10,
914	12
200	14
861	11	p.F861WfsX90, c.2582_2583delTT,
220	6	T220I,