D1689N Summary

SCN5A D1689N was found in 0 papers (see below) with a total of 1 carrier: 0 had BrS1, 0 had LQT3, and 0 had other disease. D1689N is present in 1 out of 251490 alleles in gnomAD (minor allele frequency of 0.000398%). D1689N has been functionally characterized in 0 papers. Other variants at the same resdue are D1689A .D1689E .D1689E .D1689G .D1689H .D1689N .D1689V .D1689Y . This residue is located in a Mild_Hotspot region for BrS1 and in a Non_Hotspot region for Long QT syndrome.

D1689N 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 0.058 -4.34 probablydamaging 0.999 0.256 4.99 2 0.669

D1689N has 55 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
280 13.6
323 13.4
324 9.1
325 10.8
326 10.5
327 12.8
329 14.6
330 14.9
331 11.8
332 10.4 A332T
333 7.9
334 9.9
335 12.6 C335R
336 12.9 P336L
375 11.7
376 12 R376H
377 14.7
378 11.7
379 7.5
380 10.7
381 12.8
382 10.4
383 6.7
384 12.5
385 14.2 A385T
386 12.9 G386E G386R G386R
387 13.4
1680 14.6 A1680T
1681 14.1 Y1681F
1682 12.3
1683 12.1
1684 6.3
1685 9.5
1686 8.6
1687 5.8
1688 5.2
1690 4.9 D1690N
1691 5.1
1692 5.3
1693 7.6
1694 11.5
1695 11.2
1696 13.2
1698 13.3 A1698T
1699 9.7
1700 13
1702 11
1703 10.3
1706 12.4
1712 13.3 G1712S
1715 11.4
1716 10.8
1718 14.1
1719 11.3
1720 14.3