We estimate the penetrance of LQTS for SCN5A T1304M around 22% and the Brugada syndrome penetrance around 4%. SCN5A T1304M was found in a total of 67 carriers in 18 papers and/or in gnomAD: 2 had Brugada syndrome, 15 had LQTS. T1304M is present in 46 alleles in gnomAD. T1304M has been functionally characterized in 22 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 (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 T1304M around 22% (15/77) and the Brugada syndrome penetrance around 4% (3/77).

PROVEAN	PolyPhen-2	BLAST-PSSM	REVEL	Penetrance Density BrS (%)	Penetrance Density LQT3 (%)
-5.3	1	0.36	0.924	7	12

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
17210841	2007	1		0	0	1	SIDS
10508990	1999	6		5	0	0
10961955	2000	1		1	0	0
10973849	2000	1		1	0	0
22360817	2012	3		3	0	0
23631430	2013	1		1	0	0
24144883	2014	1		0	0	1	AF
24631775	2014	1		0	0	1	SIDS
25210526	2014	2		0	2	0
26669661	2016	4		2	0	0
26746457	2016	1		0	0	0
27566755	2016	9		9	0	0
22685113	2012	1		0	0	1	AF
19716085	2009	3		3	0	0
29325976	2018	1		0	1	0
29764897	2018	1		0	0	0
30059973	2018	2		2	0	0
LITERATURE, COHORT, AND GNOMAD:	-	67	50	15	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)
27566755	2016
22685113	2012	HEK
29325976	2018
24613995	2014	HEK	68	-0.3	0.6	81
10508990	1999
10961955	2000
10973849	2000
22360817	2012
23631430	2013
24144883	2014
24631775	2014
25210526	2014
26669661	2016
18451998	2008	tsA201	100
17210841	2007	tsA206	100	6.7	11.2	718
29017927	2017
28412158	2017
17646591	2007
26746457	2016
19716085	2009
29764897	2018
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
1218	11	S1218I, S1218T,
1281	9	c.3840+1G>A, V1281F,
1304	0	T1304M,
1243	11	D1243N,
1274	12
1216	14	L1216V,
1285	12
1299	12	c.3894delC,
1220	12	G1220E,
1673	6
1675	9
1283	15	L1283M,
1309	11	R1309H, R1309C,
1226	11
1747	15	V1747M,
1669	10
1671	10
1221	12	A1221V,
1242	13
1668	15	M1668T,
1676	10	M1676I, M1676T,
1219	10	S1219N,
1672	10	S1672Y,
1279	13	V1279I,
1239	12	L1239P,
1310	12
1306	7	R1306S, R1306H,
1305	4
1680	15	A1680P, A1680T,
1246	13
1282	11	S1282A,
1302	6	p.L1302Vfs18,
1247	14	T1247I,
1307	6
1678	10	N1678S,
1223	11	c.3667delG,
1697	15
1275	13	D1275N,
1222	8	p.L1222LfsX7, L1222R,
1300	10
1674	7	F1674V,
1215	12	I1215V,
1301	5
1284	13
1700	15
1280	14
1751	13
1311	13	L1311P,
1677	8
1308	7	L1308F,
1250	13
1224	14
1670	8
1240	13	E1240Q,
1225	10	E1225K, G1225K,
1278	9	I1278N,
1679	13
1277	12
1667	13	V1667I,
1303	6	R1303Q, R1303W,
1666	13