We estimate the penetrance of LQTS for KCNH2 A32S is 28%. We are unaware of any observations of this variant in individuals. A32S is not present in gnomAD. We have tested the trafficking efficiency of this variant, 76% of WT with a standard error of 24%; in our analysis we used SE < 20% as 'high quality'. Approximately below 50% of WT is considered PS3 moderate and below 30% is PS3 strong. A32S has not been functionally characterized. This residue is located in a Hotspot region for LQT2. In silico predictions, functional data (if available), and location in structure are equivalent to observing 2 individuals with LQT2 and 8 unaffected individuals.These data combined with observations of carriers lead us to estimate the LQTS penetrance for KCNQ1 A32S around 28% (2/10).

PROVEAN	PolyPhen-2	BLAST-PSSM	REVEL	Penetrance Density (%)
-1.857	0.998	0	0.759	79

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 LQTS probability density in a shell of residues surrounding a residue of interest (Kroncke et al. 2019).

PubMed ID	Year	Carriers	Unaffected	LQT2	Other Disease
LITERATURE, COHORT, AND GNOMAD:	-	0	0	0	-
VARIANT FEATURES ALONE:	-	10	8	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.

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. NOTE: some residues appear multiple times at different distances since the functional K_V11.1 channel (protein product of KCNH2/hERG) is a homotetramer and occasionally the same residue from multiple subunits is present within the 15A window. 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
32	0	A32T,
31	4	I31S,
33	5	N33T,
125	5
124	5	M124R, M124T,
40	5
41	6	V41A,
42	6	I42N,
39	6	C39R, C39X,
64	7	C64Y, C64R,
34	7	A34T,
30	7	I30Del, I30T,
126	8
127	8
36	8	V36X,
123	8
795	9	V795I,
796	9	V796Del, V796L, V796L,
63	9	P63H,
86	9	L86R,
35	9	R35W,
43	9	Y43D, Y43C,
122	10
115	10	V115M,
114	10	P114S,
797	10	A797T,
798	10	I798fsX,
60	10	M60T,
15	10	L15V,
38	10
29	11	F29S, F29V, F29L, F29L, F29L,
65	11	T65P,
113	11	V113Del,
112	11	V112M,
44	11	C44W, C44F, C44X,
794	11	V794I, V794D,
61	11	Q61R,
66	11	C66R, C66Y, C66G,
59	12
62	12	R62Q,
14	12
18	12	I18M,
37	12
85	13	A85V, A85P,
788	13	E788D, E788D, E788K,
19	13	I19F,
128	13	N128S,
12	13	N12D,
87	13	L87P,
82	13	I82T, I82dup, I82Ins, I82Del,
83	13	A83fsX, A83P,
116	13	K116Q,
48	13
121	13	A121fsX,
129	13	F129C,
789	13
111	14	D111V,
45	14	N45D, N45K, N45K,
89	14	A89V, A89G,
790	14
110	14	V110A,
56	14	R56Q,
90	14	E90K,
22	14	F22S, F22Y,
791	14	R791W, R791Q,
799	14	L799sp,
88	15
860	15