KCNH2 Variant G487S Detail

We estimate the penetrance of LQTS for KCNH2 G487S is 3%. This variant was found in a total of 26 carriers in 1 papers or gnomAD, 0 had LQTS. G487S is present in 24 alleles in gnomAD. G487S has not been functionally characterized. This residue is located in a Mild_Hotspot region for LQT2. In silico predictions, functional data (if available), and location in structure are equivalent to observing 1 individuals with LQT2 and 9 unaffected individuals.These data combined with observations of carriers lead us to estimate the LQTS penetrance for KCNQ1 G487S around 3% (1/36).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-1.834 0.635 0 0.536 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 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
26746457 2016 1 1
LITERATURE, COHORT, AND GNOMAD: - 26 26 0 -
VARIANT FEATURES ALONE: - 10 9 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.

G487S has 24 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
487 0 G487R, G487S,
486 4
488 5 R488C, R488H,
489 6 I489F, I489I,
490 6 A490P, A490T,
491 7 V491I,
485 7 H485X,
484 8
483 10 V483I,
471 10 F471X,
472 10 R472X, R472C,
492 10 H492Y,
494 11 F494Del,
475 11 Y475Del, Y475C,
493 12 Y493F, Y493C, Y493Ins, Y493H,
473 12 T473P,
474 12 T474I,
399 13
398 13 W398X, W398L,
482 14 V482A,
470 14 N470D,
477 14
480 14 E480V,
400 15 I400N,