G546R Summary

KCNH2 G546R was found in 0 papers (see below) with a total of 0 carriers: 0 had LQT2. G546R is not present in gnomAD. G546R has been functionally characterized in 1 paper. This residue is located in a Non_Hotspot region for LQT2.

In silico predictions, functional data (if available), and location in structure are equivalent to observing 9 individuals unaffected with LQT2 and 1 individuals affected with LQT2.

G546R Reported Clinical Data

PMID Year Carriers Unaffected LQT2 Other disease
Summary totals might not agree with the literature table because of duplicate patients, which were excluded from the total counts.

G546R Reported Functional Data: heterozygously 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).

PMID Year Cell type S.S. peak current (%WT) Peak tail current (%WT) V0.5 act V0.5 inact Rec. inact. (%WT) Deactivation (%WT)
21044581 2010 Xeno

G546R Reported Functional Data: homozygously collected

PMID Year Cell type S.S. peak current (%WT) Peak tail current (%WT) V0.5 act V0.5 inact Rec. inact. (%WT) Deactivation (%WT)
21044581 2010 Xeno -30.10

G546R Predictions

PROVEAN scores less than -2 are considered deleterious. REVEL scores higher than 0.5 or 0.75 is 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. PAM scores reflect the chemistry difference between WT and variant amino acid (more negative being greater difference between the two). BLAST-PSSM reflects the evolutionary conservation of residue substitutions, more negative numbers indicate fewer observations of the specific substitution than is expected.

PAM Score REVEL Score PROVEAN Score Polyphen2 Score BLAST-PSSM
-9 0.95 -7.668 1 -2

G546R has 41 neighbors (found in individuals) within 15 ångströms

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. This results from the fact that the functional Kv11.1 channel 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.

ResidueNumber Distance(Å) Variants
412 12.4 W412X
539 12.6
540 12.3 D540fsX
541 13.4 R541C R541H
542 11.2
543 7.4 S543fsX
544 8.2 E544A E544fsX
545 5.9
547 3.3 A547T
548 4.9
549 5 V549M
550 7
551 10 F551L
552 10.1 L552S
553 10.6 L553V
554 13
555 14.1
655 14.6
657 14.4 G657S G657V
658 11.8
659 10.5
660 12.7 S660L
661 10.6 A661V
662 6.6
663 9.4
664 12.2 Q664X
665 6.9 R665Q
666 6.2
667 10.3 Y667X
668 12 S668L
669 14.4 G669C G669R G669X
670 14.4
671 13.4 A671Del A671G
673 13.8
674 9.6 H674fsX H674Y
675 12
677 12.4 M677T
678 9.6
681 10.9 R681W
682 13 E682X
685 13.7 R685C R685H R685P