A1017S Summary

KCNH2 A1017S was found in 0 papers (see below) with a total of 1 carrier: 0 had LQT2. A1017S is present in 1 out of 156338 alleles in gnomAD (0.00064%). A1017S has been functionally characterized in 0 papers. 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.


A1017S 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.

A1017S 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
0 0.593 -0.038 0.02 2

A1017S has 30 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
1002 14.7 G1002E
1003 14.2 D1003H D1003Y
1004 13.7 S1004I S1004T
1005 13.2 R1005fsX R1005Q
1006 12.6 G1006fsX G1006V
1007 12 R1007C R1007H
1008 11.4
1009 10.7 Y1009X
1010 10.1
1011 9.3 E1011K
1012 8.5 L1012fsX
1013 7.6
1014 6.6 R1014fsX R1014X
1015 5.4 C1015Y
1016 3.8
1018 3.8 P1018A P1018L
1019 5.4
1020 6.6
1021 7.6 S1021fsX S1021N
1022 8.5
1023 9.3 L1023Del L1023P
1024 10.1
1025 10.7
1026 11.4 P1026R
1027 12 L1027I
1028 12.6 S1028Del
1029 13.2 S1029fsX
1030 13.7 P1030L P1030X
1031 14.2 G1031C G1031fsX G1031X
1032 14.7 R1032fsX R1032P R1032Q R1032W R1032X