T559R Summary

SCN5A T559R was found in 0 papers (see below) with a total of 1 carrier: 0 had BrS1, 0 had LQT3, and 0 had other disease. T559R is present in 1 out of 249138 alleles in gnomAD (minor allele frequency of 0.000401%). T559R has been functionally characterized in 0 papers. Other variants at the same resdue are T559A .T559I .T559K .T559P .T559R .T559S . This residue is located in a Non_Hotspot region for BrS1 and in a Non_Hotspot region for Long QT syndrome.

T559R 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 0.087 -1.14 probablydamaging 0.966 3.741 -0.58 -6 0.325

T559R 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
544 14.7
545 14.2
546 13.7
547 13.2
548 12.6
549 12
550 11.4
551 10.7 A551T A551V
552 10.1 G552R G552R G552W
553 9.3
554 8.5
555 7.6 E555K
556 6.6
557 5.4 H557Y
558 3.8 H558R
560 3.8
561 5.4
562 6.6
563 7.6
564 8.5
565 9.3
566 10.1
567 10.7 L567Q
568 11.4 R568C R568H
569 12 R569Q R569W
570 12.6 T570N
571 13.2 S571I
572 13.7 A572D A572F A572S A572V
573 14.2 Q573E
574 14.7