A551T Summary

SCN5A A551T was found in 4 papers (see below) with a total of 3 carriers: 2 had BrS1, 0 had LQT3, and 0 had other disease. A551T is not present in gnomAD. A551T has been functionally characterized in 2 papers. Other variants at the same resdue are A551E .A551G .A551P .A551S .A551T .A551V . Given the functional data available, we estimate this variant has "Partial_LOF" in vitro character. (LOF and GOF denote loss-of-function and gain-of-function, respectively). This residue is located in a Mild_Hotspot region for BrS1 and in a Non_Hotspot region for Long QT syndrome.

A551T Reported Clinical Data

PMID Year Unaffected BrS LQT3 Other Other disease
2446357820140100
1970615920090100
1615573520051200
2615475420150100
Summary totals might not agree with the literature table because of duplicate patients, which were excluded from the total counts.

A551T Reported Functional Data

Peak current and late current are relative % to wildtype. V0.5 act/inact are the voltages at which half of the maximal current is reached during an activation and inactivation protocol, each is in units of mV and relative to wildtype.

PMID Year Cell type Peak current V0.5 act V0.5 inact Rec from inact Late current
24463578 2014 HEK 38.9 -1.8 -1.4 NA
19706159 2009 HEK 58.3 0 -5 NA

A551T 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 0.35 -0.54 possiblydamaging 0.801 3.213 0.09 -1 0.563

A551T 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
536 14.7 D536H
537 14.2
538 13.7
539 13.2
540 12.6
541 12
542 11.4
543 10.7
544 10.1
545 9.3
546 8.5
547 7.6
548 6.6
549 5.4
550 3.8
552 3.8 G552R G552R G552W
553 5.4
554 6.6
555 7.6 E555K
556 8.5
557 9.3 H557Y
558 10.1 H558R
559 10.7 T559I
560 11.4
561 12
562 12.6
563 13.2
564 13.7
565 14.2
566 14.7