We estimate the penetrance of LQTS for SCN5A R1644H around 64% and the Brugada syndrome penetrance around 7%. SCN5A R1644H was found in a total of 24 carriers in 15 papers and/or in gnomAD: 1 had Brugada syndrome, 17 had LQTS. R1644H is not present in gnomAD. R1644H has been functionally characterized in 17 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 (1 with LQTS). These data combined with observations of carriers lead us to estimate the LQTS penetrance for SCN5A R1644H around 64% (18/34) and the Brugada syndrome penetrance around 7% (2/34).

PROVEAN	PolyPhen-2	BLAST-PSSM	REVEL	Penetrance Density BrS (%)	Penetrance Density LQT3 (%)
-4.56	0.995	-0.14	0.974	22	38

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
26803770	2016	15		10	0	0
8541846	1995	2		2	0	0
15051636	2004	2		1	0	0
15840476	2005	2		2	0	0
19026623	2009	1		1	0	0
20541041	2010	1		1	0	0
22360817	2012	1		1	0	0
23631430	2013	1		1	0	0
26669661	2016	16		11	0	0
26940925	2016	1		1	0	0
28341781	2017	1		0	1	0
25904541	2015	1		1	0	0
27566755	2016	2		2	0	0
29691127	2018	1		1	0	0
30059973	2018	2		2	0	0
LITERATURE, COHORT, AND GNOMAD:	-	24	6	17	1		-
VARIANT FEATURES ALONE:	-	15	13	1	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)
29691127	2018
30059973	2018
8541846	1995
15051636	2004
15840476	2005
19026623	2009
20541041	2010
22360817	2012
23631430	2013
26669661	2016
26803770	2016	hiPSC-CM	163
26940925	2016
28341781	2017
29017927	2017
25904541	2015
27566755	2016
8917568	1996	Oocytes		-6.4	-2.5	800

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
1643	7	I1643L,
1778	12
1653	15
1635	10
1652	12	M1652T, M1652R,
1634	8	L1634P,
1650	11	L1650F,
1641	6
1639	7	G1639A,
1779	13	T1779M,
1787	10	S1787N,
1654	15
1786	14	L1786Q, L1786R, c.5356_5357delCT,
1648	7
1649	10	A1649V,
1644	0	R1644L, R1644C, R1644H,
1640	7
256	12
1793	11	M1793K,
1781	14	E1781G, E1781D,
1789	6
1632	15	R1632C, R1632H, R1632L,
255	13
1645	5	T1645M,
1796	13
1788	10	c.5361_5364delTGAG,
1638	6	R1638X, R1638Q,
1651	9
259	14
1633	11
1791	13
1637	5
253	13
1792	10	D1792V, D1792N, D1792Y,
1636	9
407	15
1775	13	p.F1775LfsX15, F1775V,
1642	7	G1642E,
1790	10	p.D1790del, D1790N, D1790G,
1631	13	G1631D,
252	12
1647	6
1822	14	c.5464-5467delTCTG, c.5464_5467delTCTG,
1646	8
1782	12