KCNH2 Variant A78T Detail

We estimate the penetrance of LQTS for KCNH2 A78T is 67%. This variant was found in a total of 1 carriers in 2 papers or gnomAD, 1 had LQTS. A78T is not present in gnomAD. A78T has been functionally characterized in 1 papers. 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 6 individuals with LQT2 and 4 unaffected individuals.These data combined with observations of carriers lead us to estimate the LQTS penetrance for KCNQ1 A78T around 67% (7/11).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-2.167 0.058 0 0.484 70
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 LQT2 Other Disease
Japan Cohort 2020 1 0 1
27761169 2016 1 1
LITERATURE, COHORT, AND GNOMAD: - 1 0 1 -
VARIANT FEATURES ALONE: - 10 4 6 -
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.

Functional Data Homozygously Collected

Steady state (S.S.) and peak tail current are relative % to wildtype (100% being no different from wildtype). V0.5 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. Recovery from inactivation (Rec. inact.) and deactivation time (Deactivation) are the ratio of characteristic time constants with wildtype (unitless).

PubMed ID Cell Type S.S Peak (%WT) Peak Tail IKr (%WT) V1/2 Act. V1/2 Inact. Recov. Inact. Deactivation (%WT)
27761169 HEK293 0 None None None None

Functional Data Heterozygously Collected

Functional parameters are the same as defined above.

PubMed ID Cell Type S.S Peak (%WT) Peak Tail IKr (%WT) V1/2 Act. V1/2 Inact. Deactivation (%WT)
27761169 HEK293 None None None

A78T has 39 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 since the functional KV11.1 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
78 0 A78T, A78P,
77 4 R77S,
79 4 A79S, A79fsX, A79T, A79Del,
81 5 Q81H, Q81P, Q81E, Q81H, Q81X,
75 5 Q75X,
80 5 A80P,
76 5
96 6 I96T, I96V,
82 7 I82Ins, I82T, I82dup, I82Del,
94 7 V94L, V94L, V94A,
74 7 T74fsX, T74M,
95 8 E95G, E95K,
97 9
83 9 A83P, A83fsX,
70 10 H70Q, H70Q, H70R,
84 10
110 10 V110A,
73 10 R73H, R73G, R73fsX, R73C,
98 10
65 11 T65P,
71 11 G71R, G71W, G71R, G71E,
85 11 A85P, A85V,
92 12 R92C, R92L,
108 12 C108Y,
109 12 L109P, L109Q, L109X,
107 13 L107P,
66 13 C66R, C66G, C66Y,
72 13 P72R, P72S, P72Q, P72T,
67 13
69 13 L69P, L69Del,
93 13 K93X, K93R,
112 13 V112M,
86 13 L86R,
99 14 Y99N, Y99S,
64 14 C64Y, C64R,
106 15 F106V, F106L, F106L, F106L,
111 15 D111V,
129 15 F129C,
127 15