We estimate the penetrance of LQTS for SCN5A T220I around 0% and the Brugada syndrome penetrance around 2%. SCN5A T220I was found in a total of 201 carriers in 15 papers and/or in gnomAD: 2 had Brugada syndrome, 0 had LQTS. T220I is present in 197 alleles in gnomAD. T220I has been functionally characterized in 21 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 T220I around 0% (0/211) and the Brugada syndrome penetrance around 2% (3/211).

PROVEAN	PolyPhen-2	BLAST-PSSM	REVEL	Penetrance Density BrS (%)	Penetrance Density LQT3 (%)
-5.85	0.999	0.82	0.961	16	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
24613995	2014	1		0	0	1	irritable bowel syndrome
14523039	2003	2		0	0	1	SSS
15671429	2005	1		0	0	1	DCM, Afib, Heart block
21273195	2011	1		0	1	0
22677073	2012	1		0	0	1	SUDS
24144883	2014	1		0	0	1	AF
25163546	2015	1		0	0	1	DCM
25171853	2014	1		0	0	1	Atrial standstill
26884609	2016	3		0	0	2	DCM
23571586	2013	1		0	0	1	stillbirth, SUDS
26636822	2015	1		0	0	1	congenital complete heart block
22685113	2012	1		0	0	1	AF
20129283	2010	1		0	1	0
20129283	2010	1		0	1	0
29325976	2018	1		0	1	0
LITERATURE, COHORT, AND GNOMAD:	-	201	199	0	2		-
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)
29325976	2018
15671429	2005
15671436	2005
21273195	2011
22677073	2012
24144883	2014
25163546	2015
25171853	2014
26884609	2016
20539757	2010
23571586	2013
24059039	2013
26636822	2015
26771585	2016
24613995	2014	HEK	48	-2.1	-7.4	62
22685113	2012	HEK
20129283	2010
20129283	2010
14523039	2003	HEK-tSA201	50	0.9	-4.4
32533946	2020	HEK	87	-2.7	-3.7
20384651	2010		65	-1.8	-6.4

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	7	V223L,
856	5	V856L,
919	15
862	11
859	5
149	15
863	12
227	14	L227P,
887	14
864	14
216	6	S216X, S216L,
851	13	c.2550_2551dupGT, F851L, p.F851CfsX19, c.2552_2553dupGT,
221	4
196	14
852	10
854	11	c.2559delT,
222	7	R222L, R222Q, R222X,
224	9	L224F,
213	14
857	8	G857D,
881	13
226	13	A226G, A226V,
921	14
860	6	p.L860fsx89,
206	12
214	13
858	9	M858L,
144	14
217	4
918	12
855	8
917	14	L917V, L917R,
913	14
199	13	S199T,
148	11
884	15
204	11	c.611+3_611+4dupAA, A204T, c.611+1G>A, A204V,
910	14	S910L,
203	9
208	15	E208K,
202	14	I202T,
853	11
161	14	E161Q, E161K,
201	14
219	6	c.656_657insATTCA, R219C, R219H, p.R219HfsX11,
225	13	R225Q, R225W,
151	13
218	7
207	11
915	14	C915R,
212	13	L212Q, L212P,
215	9	p.L215CfsX10,
914	11
200	10
861	9	c.2582_2583delTT, p.F861WfsX90,
145	14
220	0	T220I,