A1870T Summary

SCN5A A1870T was found in 1 paper (see below) with a total of 3 carriers: 0 had BrS1, 1 had LQT3, and 0 had other disease. A1870T is present in 2 out of 249268 alleles in gnomAD (minor allele frequency of 0.000802%). A1870T has been functionally characterized in 0 papers. Other variants at the same resdue are A1870D .A1870G .A1870P .A1870S .A1870T .A1870V . This residue is located in a Mild_Hotspot region for BrS1 and in a Mild_Hotspot region for Long QT syndrome.

A1870T Reported Clinical Data

PMID Year Unaffected BrS LQT3 Other Other disease
2363143020130010
Summary totals might not agree with the literature table because of duplicate patients, which were excluded from the total counts.

A1870T 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
Tolerated 0.166 -1.58 benign 0.438 1.576 -0.98 -1 0.61

A1870T has 19 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
1490 14.7
1494 14.9
1784 14.8 E1784K
1859 12.7
1862 12.3
1863 10.3
1864 13.6
1865 12.3
1866 8.8
1867 5
1868 7.2
1869 4.3
1871 3.8
1872 6.5
1873 8.7
1874 9.2
1875 14.2 p.M1875dup
1877 11.6
1878 14