We estimate the penetrance of LQTS for SCN5A R225W around 20% and the Brugada syndrome penetrance around 24%. SCN5A R225W was found in a total of 24 carriers in 11 papers and/or in gnomAD: 6 had Brugada syndrome, 5 had LQTS. R225W is present in 6 alleles in gnomAD. R225W has been functionally characterized in 13 papers. This residue is located in a Mild_Hotspot region for Brugada syndrome and a Mild_Hotspot region for LQTS. In silico predictions, functional data (if available), and location in structure are equivalent to phenotyping 10 individuals for Brugada syndrome (2 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 R225W around 20% (5/34) and the Brugada syndrome penetrance around 24% (8/34).

PROVEAN	PolyPhen-2	BLAST-PSSM	REVEL	Penetrance Density BrS (%)	Penetrance Density LQT3 (%)
-7.8	1	-6.48	0.953	15	20

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
29167113	2018	1		0	0	1	IBS
12574143	2003	2		0	0	1	DCM, conduction
19606473	2009	1		0	1	0
20031634	2009	10		0	4	0
22360817	2012	1		1	0	0
22885917	2012	2		0	2	0
19251209	2009	1		0	1	0
19716085	2009	4		4	0	0
20129283	2010	2		0	2	0
20129283	2010	1		0	1	0
30059973	2018	4		4	0	0
LITERATURE, COHORT, AND GNOMAD:	-	24	13	5	6		-
VARIANT FEATURES ALONE:	-	15	13	0	2	-	-

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)
20031634	2009
22360817	2012
22885917	2012
25624448	2015
19251209	2009
12574143	2003	Xeno	10	14	11.1
19716085	2009
20129283	2010
20129283	2010
30059973	2018
24573164	2014	HEK	88		-1.81
29167113	2018	HEK	6	17.5	9.2
19606473	2009

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
848	12	I848F,
223	8	V223L,
856	14	V856L,
231	11	c.692_693delCA,
198	10
147	13
193	10	W193X, W193R,
164	10	F164L,
195	11
170	14	F170I,
228	6	K228R,
138	8	M138I,
227	7	L227P,
143	11
171	9
137	8	I137V,
142	10
197	6
229	8
163	14	c.486delC,
851	12	c.2550_2551dupGT, p.F851CfsX19, c.2552_2553dupGT, F851L,
221	11
196	7
169	12
189	15
852	11
222	9	R222X, R222L, R222Q,
224	7	L224F,
232	13	V232I, V232F,
133	13
160	15	p.V160fs,
191	14
134	12	N134S,
849	14
226	6	A226V, A226G,
205	15	Y205X, c.612-2A>G,
166	13	A166T,
144	8
855	13
172	12
230	11	I230T, I230V, I230M,
199	9	S199T,
139	11	p.I137_C139dup,
148	11
165	11
204	11	c.611+3_611+4dupAA, c.611+1G>A, A204T, A204V,
146	14	V146A, V146M,
203	11
192	13
136	13	L136P,
168	7
175	12	K175N,
202	12	I202T,
194	10
141	5	I141N, I141V,
188	14
135	14	M135V,
167	11
161	13	E161K, E161Q,
201	8
219	14	c.656_657insATTCA, R219H, R219C, p.R219HfsX11,
225	0	R225Q, R225W,
218	14
207	15
200	6
145	10
140	9
220	13	T220I,