Home Structure Report ENSP00000344055.4_3 monomer AF-O14617-F1 monomer 4afi monomer 4afi dimer
Date 2024-01-02
Case SampleCase
Gene AP3D1
Protein O14617-1
Variant V699M

V699 Rate4Site Score ENST00000345016.9

Rate4Site Score QQ-Interval Std MSA
Normalized: -0.28 -0.44, -0.27 0.22 98.00/100

MusiteDeep (PTMs) within 8.0A of V699

PTM Residue PTM Type Probability
696 Phosphothreonine 0.7

Structure Summary

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 ENSP00000344055.4_3 A 4afi 100.0 1.0 696 729
alphafold AF-O14617-F1 A 0.0 1.0 76.63 35.66 1 1153 -0.5 0.26 -0.01 0.297
X-RAY 4afi A 2.8 1.0 696 729 -0.95 -0.08
X-RAY 4afi A 2.8 1.0 696 729 -0.07 1.0

ENSP00000344055.4_3.A monomer - Structure Detail

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 ENSP00000344055.4_3 A 4afi 100.0 1.0 696 729

clinvar Results - ENSP00000344055.4_3.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-4.09 30.00 0.00 0.00 0.00 0.00 0.00 0.89 0.00

COSMIC Results - ENSP00000344055.4_3.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-1.51 28.00 0.00 0.00 0.00 0.00 0.00 0.87 0.00

Location of V699M in ENSP00000344055.4_3.A (NGL Viewer)

Variant Distributions

5 gnomAD38
clinvar
No clinvar Variants map to this structure
2 COSMIC

Ripley's Univariate K

gnomAD38
clinvar
Ripley's Univariate K graphic was not created for clinvar
COSMIC
Ripley's Univariate K graphic was not created for COSMIC

Ripley's Bivariate D

clinvar - gnomAD38
clinvar-gnomAD38 Bivariate D plot was not created
COSMIC - gnomAD38
COSMIC-gnomAD38 Bivariate D plot was not created

PathProx (clinvar - gnomAD38) Results

PathProx
No graphic was created
PathProx clinvar ROC
No graphic was created
PathProx clinvar PR
No graphic was created

PathProx (COSMIC - gnomAD38) Results

PathProx
No graphic was created
PathProx COSMIC ROC
No graphic was created
PathProx COSMIC PR
No graphic was created

AF-O14617-F1.A monomer - Structure Detail

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-O14617-F1 A 0.0 1.0 76.63 35.66 1 1153 -0.5 0.26 -0.01 0.297

clinvar Results - AF-O14617-F1.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-2.65 28.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00

COSMIC Results - AF-O14617-F1.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-2.72 28.00 -2.27 10.00 0.45 0.30 -0.01 1.00 0.00

Location of V699M in AF-O14617-F1.A (NGL Viewer)

Variant Distributions

183 gnomAD38
clinvar
No clinvar Variants map to this structure
57 COSMIC

Ripley's Univariate K

gnomAD38
clinvar
Ripley's Univariate K graphic was not created for clinvar
COSMIC

Ripley's Bivariate D

clinvar - gnomAD38
clinvar-gnomAD38 Bivariate D plot was not created
COSMIC - gnomAD38

PathProx (clinvar - gnomAD38) Results

PathProx
No graphic was created
PathProx clinvar ROC
No graphic was created
PathProx clinvar PR
No graphic was created

PathProx (COSMIC - gnomAD38) Results

PathProx
PathProx COSMIC ROC
PathProx COSMIC PR

4afi.A monomer - Structure Detail

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 4afi A 2.8 1.0 696 729 -0.95 -0.08

clinvar Results - 4afi.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-4.89 36.00 0.00 0.00 0.00 0.00 0.00 0.92 0.00

COSMIC Results - 4afi.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-6.21 36.00 0.00 0.00 0.00 0.00 0.00 0.90 0.00

Location of V699M in 4afi.A (NGL Viewer)

Variant Distributions

5 gnomAD38
clinvar
No clinvar Variants map to this structure
2 COSMIC

Ripley's Univariate K

gnomAD38
clinvar
Ripley's Univariate K graphic was not created for clinvar
COSMIC
Ripley's Univariate K graphic was not created for COSMIC

Ripley's Bivariate D

clinvar - gnomAD38
clinvar-gnomAD38 Bivariate D plot was not created
COSMIC - gnomAD38
COSMIC-gnomAD38 Bivariate D plot was not created

PathProx (clinvar - gnomAD38) Results

PathProx
No graphic was created
PathProx clinvar ROC
No graphic was created
PathProx clinvar PR
No graphic was created

PathProx (COSMIC - gnomAD38) Results

PathProx
No graphic was created
PathProx COSMIC ROC
No graphic was created
PathProx COSMIC PR
No graphic was created

4afi.A dimer - Structure Detail

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 4afi A 2.8 1.0 696 729 -0.07 1.0

clinvar Results - 4afi.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-2.66 27.00 0.00 0.00 0.00 0.00 0.00 0.95 0.00

COSMIC Results - 4afi.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-2.60 36.00 5.10 5.00 1.00 1.00 -0.07 1.00 0.00

Location of V699M in 4afi.A (NGL Viewer)

Variant Distributions

9 gnomAD38
clinvar
No clinvar Variants map to this structure
4 COSMIC

Ripley's Univariate K

gnomAD38
clinvar
Ripley's Univariate K graphic was not created for clinvar
COSMIC

Ripley's Bivariate D

clinvar - gnomAD38
clinvar-gnomAD38 Bivariate D plot was not created
COSMIC - gnomAD38

PathProx (clinvar - gnomAD38) Results

PathProx
No graphic was created
PathProx clinvar ROC
No graphic was created
PathProx clinvar PR
No graphic was created

PathProx (COSMIC - gnomAD38) Results

PathProx
PathProx COSMIC ROC
PathProx COSMIC PR