A1698T Summary

SCN5A A1698T was found in 2 papers (see below) with a total of 4 carriers: 1 had BrS1, 0 had LQT3, and 0 had other disease. A1698T is present in 3 out of 251490 alleles in gnomAD (minor allele frequency of 0.001193%). A1698T has been functionally characterized in 0 papers. Other variants at the same resdue are A1698D .A1698G .A1698P .A1698S .A1698T .A1698V . This residue is located in a Mild_Hotspot region for BrS1 and in a Non_Hotspot region for Long QT syndrome.

A1698T Reported Clinical Data

PMID Year Unaffected BrS LQT3 Other Other disease
2012928320100100
2932597620180100
Summary totals might not agree with the literature table because of duplicate patients, which were excluded from the total counts.

A1698T 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 0.002 -2.43 probablydamaging 1 1.691 -1.6 -1 0.872

A1698T has 64 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
329 13.8
330 11.1
331 8.3
332 11.8 A332T
333 12.7
378 11.7
379 13.5
381 15
382 10.8
383 14.4
385 14.4 A385T
386 11 G386E G386R G386R
387 6.5
388 10.5
389 13.5
390 8.8
391 12.8
393 14.5
394 13.5
1219 14.8
1220 13.1
1221 14.2 A1221V
1222 13.9
1223 9.3
1224 9.8
1225 13.5 E1225K
1226 11.1
1227 11.4
1228 10.5 Y1228C Y1228H
1665 11.8
1666 14.8
1667 14.8 V1667I
1668 10.2
1669 10.9
1670 14.2
1671 14.5
1672 8.7 S1672Y
1673 11.3
1675 12.5
1676 9.4 M1676I M1676I M1676I
1677 14.6
1679 13.7
1680 13.8 A1680T
1688 13.6
1689 13.3
1690 12.9 D1690N
1691 9.1
1692 9.1
1693 8.1
1694 9.2
1695 9.5
1696 4.8
1697 3.8
1699 3.8
1700 5.1
1701 5.2 M1701I M1701I M1701I
1702 5.7
1703 8.4
1704 9.6
1705 9.8
1706 12.4
1707 13.6
1708 14.7
1716 15