KCNH2 Variant H492R Detail

We estimate the penetrance of LQTS for KCNH2 H492R is 53%. We are unaware of any observations of this variant in individuals. H492R is not present in gnomAD. H492R 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 5 individuals with LQT2 and 5 unaffected individuals.These data combined with observations of carriers lead us to estimate the LQTS penetrance for KCNQ1 H492R around 53% (5/10).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-7.297 0.786 0 0.903 61
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
LITERATURE, COHORT, AND GNOMAD: - 0 0 0 -
VARIANT FEATURES ALONE: - 10 5 5 -
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.

H492R 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
492 0 H492Y,
491 6 V491I,
475 6 Y475C, Y475Del,
493 6 Y493H, Y493C, Y493F, Y493Ins,
489 6 I489I, I489F,
490 7 A490P, A490T,
496 7
494 8 F494Del,
495 8 K495X,
477 8
497 9 W497L, W497X,
476 10 V476I,
483 10 V483I,
488 10 R488H, R488C,
471 10 F471X,
470 10 N470D,
498 10
487 10 G487S, G487R,
474 11 T474I,
473 11 T473P,
537 11 R537W,
478 11 A478D,
480 11 E480V,
484 12
486 12
479 13
499 13
482 13 V482A,
501 13 D501Y, D501H, D501N,
481 13
402 13 H402R,
467 14
485 14 H485X,
472 14 R472X, R472C,
500 14 I500Del,
538 14
469 14
4 15
534 15 R534C,