D84N Summary

SCN5A D84N was found in 3 papers (see below) with a total of 2 carriers: 2 had BrS1, 0 had LQT3, and 0 had other disease. D84N is not present in gnomAD. D84N has been functionally characterized in 1 paper. Other variants at the same resdue are D84A .D84E .D84E .D84G .D84H .D84N .D84V .D84Y . 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.

D84N Reported Clinical Data

PMID Year Unaffected BrS LQT3 Other Other disease
2012928320100200
2932597620180100
3253394620200000
Summary totals might not agree with the literature table because of duplicate patients, which were excluded from the total counts.

D84N 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
32533946 2020 HEK 32.8 7.9 NA

D84N 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 -4.55 probablydamaging 0.993 0.05012 1.2 2 0.949

D84N 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
69 14.7 G69D
70 14.2 N70K N70K N70S
71 13.7
72 13.2
73 12.6
74 12 E74D E74D
75 11.4
76 10.7
77 10.1
78 9.3
79 8.5 P79A
80 7.6
81 6.6
82 5.4 D82E D82E
83 3.8
85 3.8
86 5.4 F86L F86L F86L
87 6.6
88 7.6 S88G
89 8.5
90 9.3
91 10.1
92 10.7 T92I
93 11.4 F93S
94 12 I94V
95 12.6 V95I V95L V95L
96 13.2
97 13.7
98 14.2
99 14.7