S554N Summary

SCN5A S554N was found in 0 papers (see below) with a total of 1 carrier: 0 had BrS1, 0 had LQT3, and 0 had other disease. S554N is present in 1 out of 249048 alleles in gnomAD (minor allele frequency of 0.000402%). S554N has been functionally characterized in 0 papers. Other variants at the same resdue are S554C .S554G .S554I .S554N .S554R .S554R .S554R .S554T . This residue is located in a Non_Hotspot region for BrS1 and in a Non_Hotspot region for Long QT syndrome.

S554N 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 0.693 0.97 probablydamaging 0.993 3.254 1.76 0 0.207

S554N 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
539 14.7
540 14.2
541 13.7
542 13.2
543 12.6
544 12
545 11.4
546 10.7
547 10.1
548 9.3
549 8.5
550 7.6
551 6.6 A551T A551V
552 5.4 G552R G552R G552W
553 3.8
555 3.8 E555K
556 5.4
557 6.6 H557Y
558 7.6 H558R
559 8.5 T559I
560 9.3
561 10.1
562 10.7
563 11.4
564 12
565 12.6
566 13.2
567 13.7 L567Q
568 14.2 R568C R568H
569 14.7 R569Q R569W