C1004R Summary
SCN5A C1004R was found in 1 paper (see below) with a total of 71 carriers: 0 had BrS1, 1 had LQT3, and 0 had other disease. C1004R is present in 70 out of 242328 alleles in gnomAD (minor allele frequency of 0.028886%). C1004R has been functionally characterized in 0 papers. Other variants at the same resdue are C1004F .C1004G .C1004R .C1004S .C1004S .C1004W .C1004Y .
This residue is located in a Non_Hotspot region for BrS1 and in a Non_Hotspot region for Long QT syndrome.
C1004R Reported Clinical Data
PMID |
Year |
Unaffected |
BrS |
LQT3 |
Other |
Other disease |
19716085 | 2009 | 0 | 0 | 1 | 0 | |
Summary totals might not agree with the literature table because of duplicate patients, which were excluded from the total counts.
C1004R 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 |
0.039 |
-3.86 |
probablydamaging |
0.998 |
3.732 |
-0.78 |
-8 |
0.723 |
C1004R 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 |
989 |
14.7 |
|
990 |
14.2 |
|
991 |
13.7 |
|
992 |
13.2 |
|
993 |
12.6 |
A993T |
994 |
12 |
|
995 |
11.4 |
L995F |
996 |
10.7 |
|
997 |
10.1 |
A997D A997S A997T |
998 |
9.3 |
|
999 |
8.5 |
|
1000 |
7.6 |
p.Gln1000del |
1001 |
6.6 |
|
1002 |
5.4 |
P1002S |
1003 |
3.8 |
|
1005 |
3.8 |
|
1006 |
5.4 |
|
1007 |
6.6 |
|
1008 |
7.6 |
P1008S |
1009 |
8.5 |
|
1010 |
9.3 |
|
1011 |
10.1 |
P1011L P1011S |
1012 |
10.7 |
|
1013 |
11.4 |
|
1014 |
12 |
P1014S |
1015 |
12.6 |
|
1016 |
13.2 |
T1016M |
1017 |
13.7 |
|
1018 |
14.2 |
|
1019 |
14.7 |
|