We estimate the penetrance of LQTS for SCN5A N1325S around 92% and the Brugada syndrome penetrance around 4%. SCN5A N1325S was found in a total of 23 carriers in 10 papers and/or in gnomAD: 0 had Brugada syndrome, 23 had LQTS. N1325S is not present in gnomAD. N1325S has been functionally characterized in 19 papers. This residue is located in a Mild_Hotspot region for Brugada syndrome and a 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 (2 with LQTS). These data combined with observations of carriers lead us to estimate the LQTS penetrance for SCN5A N1325S around 92% (25/33) and the Brugada syndrome penetrance around 4% (1/33).

PROVEAN	PolyPhen-2	BLAST-PSSM	REVEL	Penetrance Density BrS (%)	Penetrance Density LQT3 (%)
-4.21	0.947	-0.41	0.923	18	72

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
8541846	1995	4		4	0	0
10973849	2000	1		1	0	0
15840476	2005	2		2	0	0
17905336	2007	1		1	0	0
17118339	2007	4		4	0	0
24342415	2014	1		1	0	0
25904541	2015	1		1	0	0
27566755	2016	21		21	0	0
19716085	2009	3		3	0	0
30059973	2018	4		4	0	0
LITERATURE, COHORT, AND GNOMAD:	-	23	0	23	0		-
VARIANT FEATURES ALONE:	-	15	12	2	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)
14736542	2004	mouse	108			238
32533946	2020	HEK	114	-9.6	-3.2
8541846	1995
10973849	2000
14736536	2004
15840476	2005
17490620	2007
17905336	2007
19762097	2011
29017927	2017
17118339	2007
17157817	2007
21677263	2011
24342415	2014
25904541	2015
27566755	2016
8917568	1996	Oocytes		1.7	2.1	3000
19716085	2009
30059973	2018

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
1328	6	V1328M,
1659	13
1271	11	W1271C,
1480	10	c.4438-1C>T, c.4437+5G>A,
1472	10	N1472S, p.N1472del,
1315	9
1314	12	c.3940_3941delCT,
1320	9	M1320I,
1333	14
1656	13
1270	13	A1270S,
1477	11	K1477N,
1471	14
1762	14	p.I1762del, I1762M,
1470	15
1478	13	K1478E,
1313	14
1660	13	I1660V, I1660S,
1329	7	G1329S,
1769	14
1316	13	R1316L, R1316Q,
1766	11	M1766T, M1766L, M1766V,
1319	10	G1319V,
1479	8
1473	9	F1473C, F1473S,
1334	14	I1334V,
1468	15	V1468F, V1468A,
1663	13
1474	13
1324	4
1481	14	G1481E, G1481R, G1481V,
1317	13	F1317C,
1327	7
1318	12
1330	9	A1330T, A1330D, A1330P,
1321	8	R1321K,
1323	6	V1323G,
1770	14	I1770V,
1482	15
1322	6	c.3963+2T>C, c.3963+4A>G,
1312	11
1326	5	A1326S,
1763	14	V1763L, V1763M,
1311	13	L1311P,
1332	12	P1332Q, P1332L,
1476	6	Q1476R, Q1476X,
1331	11	I1331V,
1475	11	Q1475L, p.Q1475NfsX6,
1469	12	I1469V,
1269	14	N1269S,
1325	0	N1325S,