C39F Summary

KCNH2 C39F was found in 0 papers (see below) with a total of 0 carriers: 0 had LQT2. C39F is not present in gnomAD. C39F has been functionally characterized in 0 papers. 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 6 individuals unaffected with LQT2 and 4 individuals affected with LQT2.


C39F 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.

C39F 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
NA 0.764 -6.595 0.565 -4

C39F has 49 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
30 11 I30Del I30T
31 9.9 I31S
32 5.7 A32T
33 5.8 N33T
34 5.7 A34T
35 7.7 R35W
36 5.3 V36X
37 7.5
38 4.9
40 4.4
41 7.4 V41A
42 9.5 I42N
43 14.3 Y43C Y43D
44 14.8 C44F C44W C44X
59 12.6
60 11.8 M60T
61 10.6 Q61R
62 10.3 R62Q
63 6.3 P63H
64 5.3 C64R C64Y
65 8.2 T65P
66 10.4 C66G C66R C66Y
67 12.5
68 14.2 F68L F68V
82 12 I82Del I82dup I82Ins I82T
83 10.5 A83fsX A83P
84 14.2
85 11.7 A85P A85V
86 7.8 L86R
87 10.4 L87P
88 13.7
89 13.9 A89G A89V
112 13 V112M
113 14.3 V113Del
114 12.7 P114S
115 13.7 V115M
121 14.4 A121fsX
122 10.8
123 10.7
124 9.3 M124R M124T
125 7.2
126 12.2
127 11.3
791 13.6 R791Q R791W
794 11.5 V794D V794I
795 11.1 V795I
796 10.3 V796Del V796L
797 13 A797T
798 14.5 I798fsX