KCNH2 Variant L550P Detail

We estimate the penetrance of LQTS for KCNH2 L550P is 14%. We are unaware of any observations of this variant in individuals. L550P is not present in gnomAD. L550P 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 L550P around 14% (1/10).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-6.709 1.0 -1 0.96 15
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 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.

L550P has 46 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
550 0
549 5 V549M,
547 5 A547T,
553 6 L553V,
548 6
551 6 F551L, F551L, F551L,
554 6
659 6
662 7
552 7 L552S,
546 7
663 8
555 9
650 9 L650X,
658 9
666 10
655 10
656 10 F656L, F656L, F656L,
660 10 S660L,
661 10 A661V,
556 10
665 11 R665Q,
543 11 S543fsX,
657 11 G657S, G657V,
557 11
545 11
654 12
667 12 Y667X,
646 12
649 12
653 12
664 13 Q664X,
542 13
558 13 A558E, A558V, A558P,
647 13
654 13
651 13 M651K,
544 14 E544fsX, E544A,
412 14 W412X,
539 14
415 14
648 14 G648A,
674 14 H674fsX, H674Y,
651 14 M651K,
559 14 L559F, L559H,
652 15 Y652X,