KCNH2 Variant D456H Detail

We estimate the penetrance of LQTS for KCNH2 D456H is 81%. We are unaware of any observations of this variant in individuals. D456H is not present in gnomAD. D456H 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 8 individuals with LQT2 and 2 unaffected individuals.These data combined with observations of carriers lead us to estimate the LQTS penetrance for KCNQ1 D456H around 81% (8/10).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-6.103 1.0 -1 0.987 90
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 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.

D456H has 48 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
456 0 D456Y,
457 5 L457P,
455 5
453 5
459 5
460 6 D460fsX,
458 7
420 7 Y420C,
454 7
452 7
528 8 R528P, R528W, R528X,
424 8
421 9 T421M, T421fsX,
425 9
525 9 K525N, K525N,
461 9
428 10 S428L, S428X, S428fsX,
417 10
451 10 P451L,
531 10 R531Q, R531W, R531Del,
450 11
463 11 F463L, F463L, F463L,
462 11 M462Ins,
507 11 P507S, P507L,
423 11
422 12 A422T,
418 12
426 12 P426H,
504 12 A504V,
505 12 A505V,
427 12 Y427S, Y427C, Y427H,
527 13
464 13 I464X,
429 13 A429P, A429V,
419 13
449 13
508 13
526 13
529 13
416 13
506 14 I506V,
522 14 G522E,
432 14
524 14
509 14 D509N,
414 15 I414fsX,
413 15 L413P,
465 15