KCNQ1 Variant C122G Detail

We estimate the penetrance of LQTS for KCNQ1 C122G is 85%. We are unaware of any observations of this variant in individuals. C122G is not present in gnomAD. C122G has not been functionally characterized. This residue is located in a Hotspot region for LQT1. In silico predictions, functional data (if available), and location in structure are equivalent to observing 8 individuals with LQT1 and 2 unaffected individuals. These data combined with observations of carriers lead us to estimate the LQTS penetrance for KCNQ1 C122G around 85% (8/10).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-7.75 0.127 1 0.841 97
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).

Reported Carrier Data

PubMed ID Year Carriers Unaffected LQT1 Other Disease
LITERATURE, COHORT, AND GNOMAD: - 0 0 0
VARIANT FEATURES ALONE: - 10 2 8 -
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.

C122G has 35 previously observed neighbors within 15 angstroms

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. This results from the fact that the functional KV7.1 channel 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
122 0 C122Y,
119 4 G119R, G119V,
113 4
121 5
117 6 P117L,
126 6 H126D,
123 6
124 6
125 7
118 7
120 7 W120C, W120C,
114 8
112 8
110 10 V110I,
127 10 F127L, F127L, F127L,
115 10 E115A, E115G,
116 10
128 11 A128del,
109 11 R109C, R109L,
129 11 V129I,
111 11 Y111C,
243 12 R243H, R243C, R243P, R243S,
108 12 G108S,
174 12 R174H, R174C, R174L,
170 12
241 12 V241F, V241I, V241G,
130 14
244 14
173 14
177 14 S177F,
106 14
131 14
107 15 Q107H, Q107H,
242 15 D242N, D242Y,
166 15 F166V,