Date | 2024-01-02 |
---|---|
Case | SampleCase |
Gene | NAGA |
Protein | P17050 |
Variant | D136N |
Rate4Site Score |
QQ-Interval |
Std |
MSA |
|
---|---|---|---|---|
Normalized: | -0.20 | -0.39, 0.02 | 0.23 | 100.00/100 |
Cosmis Score |
pValue |
cossyn |
source |
|
---|---|---|---|---|
Normalized: | 3.13 | 1.00 | -0.83 | PDB |
PTM Residue |
PTM Type |
Probability |
---|---|---|
124 | N-linked_glycosylation | 0.9 |
Binding Site Probability |
---|
0.2 |
Method |
Structure Id |
Chain |
PDB Template |
PDB Resolution |
Template Identity |
Transcript Identity |
AF Global Quality |
AF Residue Confidence |
Seq Start |
Seq End |
ddG Monomer |
ddG Cartesian |
Pathprox clinvar |
Pathprox clinvar AOC |
Pathprox COSMIC |
Pathprox COSMIC AOC |
PDB Pos |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
swiss | P17050_19_404_1ktb.1.B | A | 1ktb.1.B | 74.87 | 1.0 | 19 | 404 | -0.67 | -0.08 | -0.01 | 0.243 | ||||||
swiss | P17050_19_404_1ktb.1.B | A | 1ktb.1.B | 74.87 | 1.0 | 19 | 404 | -0.01 | 0.243 | ||||||||
modbase | ENSP00000379680.3_1 | A | 4do4 | 100.0 | 1.0 | 18 | 411 | -0.66 | 0.37 | 0.11 | 0.364 | ||||||
alphafold | AF-P17050-F1 | A | 0.0 | 1.0 | 96.27 | 98.65 | 1 | 411 | -2.36 | 0.78 | -0.01 | 0.259 | |||||
X-RAY | 4do6 | A | 1.6 | 1.0 | 18 | 405 | -0.01 | 0.252 | |||||||||
X-RAY | 4do4 | B | 1.4 | 1.0 | 18 | 411 | -0.69 | 0.26 | -0.01 | 0.251 |
Method |
Structure Id |
Chain |
PDB Template |
PDB Resolution |
Template Identity |
Transcript Identity |
AF Global Quality |
AF Residue Confidence |
Seq Start |
Seq End |
ddG Monomer |
ddG Cartesian |
Pathprox clinvar |
Pathprox clinvar AOC |
Pathprox COSMIC |
Pathprox COSMIC AOC |
PDB Pos |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
swiss | P17050_19_404_1ktb.1.B | A | 1ktb.1.B | 74.87 | 1.0 | 19 | 404 | -0.67 | -0.08 | -0.01 | 0.243 |
Neutral Kz |
Neutral Kt |
Pathogenic Kz |
Pathogenic Kt |
ROC AUC |
PR AUC |
PathProx |
Neutral Constraint |
Pathogenic Constraint |
---|---|---|---|---|---|---|---|---|
1.38 | 5.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.97 | 0.00 |
Neutral Kz |
Neutral Kt |
Pathogenic Kz |
Pathogenic Kt |
ROC AUC |
PR AUC |
PathProx |
Neutral Constraint |
Pathogenic Constraint |
---|---|---|---|---|---|---|---|---|
1.07 | 17.00 | -1.41 | 8.00 | 0.36 | 0.24 | -0.01 | 1.00 | 0.00 |
Method |
Structure Id |
Chain |
PDB Template |
PDB Resolution |
Template Identity |
Transcript Identity |
AF Global Quality |
AF Residue Confidence |
Seq Start |
Seq End |
ddG Monomer |
ddG Cartesian |
Pathprox clinvar |
Pathprox clinvar AOC |
Pathprox COSMIC |
Pathprox COSMIC AOC |
PDB Pos |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
swiss | P17050_19_404_1ktb.1.B | A | 1ktb.1.B | 74.87 | 1.0 | 19 | 404 | -0.01 | 0.243 |
Neutral Kz |
Neutral Kt |
Pathogenic Kz |
Pathogenic Kt |
ROC AUC |
PR AUC |
PathProx |
Neutral Constraint |
Pathogenic Constraint |
---|---|---|---|---|---|---|---|---|
-2.52 | 41.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.98 | 0.00 |
Neutral Kz |
Neutral Kt |
Pathogenic Kz |
Pathogenic Kt |
ROC AUC |
PR AUC |
PathProx |
Neutral Constraint |
Pathogenic Constraint |
---|---|---|---|---|---|---|---|---|
-2.62 | 41.00 | -2.08 | 8.00 | 0.36 | 0.24 | -0.01 | 1.00 | 0.00 |
Method |
Structure Id |
Chain |
PDB Template |
PDB Resolution |
Template Identity |
Transcript Identity |
AF Global Quality |
AF Residue Confidence |
Seq Start |
Seq End |
ddG Monomer |
ddG Cartesian |
Pathprox clinvar |
Pathprox clinvar AOC |
Pathprox COSMIC |
Pathprox COSMIC AOC |
PDB Pos |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
modbase | ENSP00000379680.3_1 | A | 4do4 | 100.0 | 1.0 | 18 | 411 | -0.66 | 0.37 | 0.11 | 0.364 |
Neutral Kz |
Neutral Kt |
Pathogenic Kz |
Pathogenic Kt |
ROC AUC |
PR AUC |
PathProx |
Neutral Constraint |
Pathogenic Constraint |
---|---|---|---|---|---|---|---|---|
1.49 | 17.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.97 | 0.00 |
Neutral Kz |
Neutral Kt |
Pathogenic Kz |
Pathogenic Kt |
ROC AUC |
PR AUC |
PathProx |
Neutral Constraint |
Pathogenic Constraint |
---|---|---|---|---|---|---|---|---|
1.37 | 17.00 | -1.24 | 24.00 | 0.62 | 0.36 | 0.11 | 0.92 | 0.12 |
Method |
Structure Id |
Chain |
PDB Template |
PDB Resolution |
Template Identity |
Transcript Identity |
AF Global Quality |
AF Residue Confidence |
Seq Start |
Seq End |
ddG Monomer |
ddG Cartesian |
Pathprox clinvar |
Pathprox clinvar AOC |
Pathprox COSMIC |
Pathprox COSMIC AOC |
PDB Pos |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
alphafold | AF-P17050-F1 | A | 0.0 | 1.0 | 96.27 | 98.65 | 1 | 411 | -2.36 | 0.78 | -0.01 | 0.259 |
Neutral Kz |
Neutral Kt |
Pathogenic Kz |
Pathogenic Kt |
ROC AUC |
PR AUC |
PathProx |
Neutral Constraint |
Pathogenic Constraint |
---|---|---|---|---|---|---|---|---|
2.21 | 17.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.97 | 0.00 |
Neutral Kz |
Neutral Kt |
Pathogenic Kz |
Pathogenic Kt |
ROC AUC |
PR AUC |
PathProx |
Neutral Constraint |
Pathogenic Constraint |
---|---|---|---|---|---|---|---|---|
1.94 | 17.00 | -1.44 | 8.00 | 0.35 | 0.26 | -0.01 | 1.00 | 0.00 |
Method |
Structure Id |
Chain |
PDB Template |
PDB Resolution |
Template Identity |
Transcript Identity |
AF Global Quality |
AF Residue Confidence |
Seq Start |
Seq End |
ddG Monomer |
ddG Cartesian |
Pathprox clinvar |
Pathprox clinvar AOC |
Pathprox COSMIC |
Pathprox COSMIC AOC |
PDB Pos |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
X-RAY | 4do6 | A | 1.6 | 1.0 | 18 | 405 | -0.01 | 0.252 |
Neutral Kz |
Neutral Kt |
Pathogenic Kz |
Pathogenic Kt |
ROC AUC |
PR AUC |
PathProx |
Neutral Constraint |
Pathogenic Constraint |
---|---|---|---|---|---|---|---|---|
-2.31 | 39.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.98 | 0.00 |
Neutral Kz |
Neutral Kt |
Pathogenic Kz |
Pathogenic Kt |
ROC AUC |
PR AUC |
PathProx |
Neutral Constraint |
Pathogenic Constraint |
---|---|---|---|---|---|---|---|---|
-2.44 | 39.00 | -2.06 | 8.00 | 0.36 | 0.25 | -0.01 | 1.00 | 0.00 |
Method |
Structure Id |
Chain |
PDB Template |
PDB Resolution |
Template Identity |
Transcript Identity |
AF Global Quality |
AF Residue Confidence |
Seq Start |
Seq End |
ddG Monomer |
ddG Cartesian |
Pathprox clinvar |
Pathprox clinvar AOC |
Pathprox COSMIC |
Pathprox COSMIC AOC |
PDB Pos |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
X-RAY | 4do4 | B | 1.4 | 1.0 | 18 | 411 | -0.69 | 0.26 | -0.01 | 0.251 |
Neutral Kz |
Neutral Kt |
Pathogenic Kz |
Pathogenic Kt |
ROC AUC |
PR AUC |
PathProx |
Neutral Constraint |
Pathogenic Constraint |
---|---|---|---|---|---|---|---|---|
1.31 | 17.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.97 | 0.00 |
Neutral Kz |
Neutral Kt |
Pathogenic Kz |
Pathogenic Kt |
ROC AUC |
PR AUC |
PathProx |
Neutral Constraint |
Pathogenic Constraint |
---|---|---|---|---|---|---|---|---|
1.17 | 17.00 | -1.39 | 8.00 | 0.35 | 0.25 | -0.01 | 1.00 | 0.00 |