P52S Summary

SCN5A P52S was found in 1 paper (see below) with a total of 3 carriers: 0 had BrS1, 1 had LQT3, and 0 had other disease. P52S is present in 2 out of 247386 alleles in gnomAD (minor allele frequency of 0.000808%). P52S has been functionally characterized in 0 papers. Other variants at the same resdue are P52A .P52H .P52L .P52R .P52S .P52T . This residue is located in a Non_Hotspot region for BrS1 and in a Mild_Hotspot region for Long QT syndrome.

P52S Reported Clinical Data

PMID Year Unaffected BrS LQT3 Other Other disease
1971608520090010
Summary totals might not agree with the literature table because of duplicate patients, which were excluded from the total counts.

P52S 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.

SIFT Sift Score PROVEAN Score Polyphen2 Polyphen2 Score eaRate blastPssm pamScore REVEL
Damaging 0.011 -6.42 benign 0.11 2.469 -0.95 -2 0.816

P52S has 30 neighbors within 15 ångströms that have been found in individuals.

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.

ResidueNumber Distance(Å) Variants
37 14.7 T37A
38 14.2
39 13.7
40 13.2
41 12.6
42 12
43 11.4 R43Q
44 10.7
45 10.1
46 9.3
47 8.5
48 7.6 E48K
49 6.6
50 5.4
51 3.8 A51V
53 3.8 R53Q
54 5.4
55 6.6
56 7.6
57 8.5
58 9.3
59 10.1
60 10.7 A60P
61 11.4
62 12
63 12.6 K63N K63N
64 13.2
65 13.7
66 14.2
67 14.7