Home Structure Report P22557-1_143_578_6hrh.1.A monomer P22557-1_143_578_6hrh.1.A trimer GENSCAN00000017881_2 monomer GENSCAN00000017881_3 monomer GENSCAN00000017881_4 monomer AF-P22557-F1 monomer 5qr1 dimer 5qr1 monomer
Date 2024-01-02
Case SampleCase
Gene ALAS2
Protein P22557-1
Variant A282T

A282 Rate4Site Score ENST00000650242.1

Rate4Site Score QQ-Interval Std MSA
Normalized: -0.62 -0.68, -0.58 0.12 100.00/100

No MusiteDeep (PTMs) predicted within 8.0A of A282

ScanNet Prediction of A282 participation in a PPI

Binding Site Probability
0.2

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
swiss P22557-1_143_578_6hrh.1.A B 6hrh.1.A 99.78 1.0 143 578 23.22 10.04 0.46 0.966 0.03 0.527
swiss P22557-1_143_578_6hrh.1.A B 6hrh.1.A 99.78 1.0 143 578 0.06 0.797 0.02 0.494
modbase GENSCAN00000017881_2 A 5qr1 99.0 1.0 140 578 17.18 10.58 0.5 0.958 -0.01 0.471
modbase GENSCAN00000017881_3 A 5txt 37.0 1.0 143 547 0.37 0.908 0.03 0.498
modbase GENSCAN00000017881_4 A 2bwn 50.0 1.0 144 540 2.66 2.81 0.29 0.889 -0.02 0.503
alphafold AF-P22557-F1 A 0.0 1.0 83.95 96.67 1 587 0.42 3.61 0.31 0.835 -0.01 0.356
X-RAY 5qr1 A 1.44 1.0 143 578 0.06 0.785 0.02 0.509
X-RAY 5qr1 B 1.44 1.0 143 578 23.53 9.62 0.49 0.954 0.03 0.528

P22557-1_143_578_6hrh.1.A.B 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
swiss P22557-1_143_578_6hrh.1.A B 6hrh.1.A 99.78 1.0 143 578 23.22 10.04 0.46 0.966 0.03 0.527

clinvar Results - P22557-1_143_578_6hrh.1.A.B

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-2.47 39.00 2.58 34.00 0.97 0.97 0.46 0.85 0.30

COSMIC Results - P22557-1_143_578_6hrh.1.A.B

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-2.46 36.00 -1.06 11.00 0.55 0.53 0.03 1.00 0.02

Location of A282T in P22557-1_143_578_6hrh.1.A.B (NGL Viewer)

Variant Distributions

38 gnomAD38
23 clinvar
22 COSMIC

Ripley's Univariate K

gnomAD38
clinvar
COSMIC

Ripley's Bivariate D

clinvar - gnomAD38
COSMIC - gnomAD38

PathProx (clinvar - gnomAD38) Results

PathProx
No graphic was created
PathProx clinvar ROC
PathProx clinvar PR

PathProx (COSMIC - gnomAD38) Results

PathProx
No graphic was created
PathProx COSMIC ROC
PathProx COSMIC PR

P22557-1_143_578_6hrh.1.A.B trimer - 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
swiss P22557-1_143_578_6hrh.1.A B 6hrh.1.A 99.78 1.0 143 578 0.06 0.797 0.02 0.494

clinvar Results - P22557-1_143_578_6hrh.1.A.B

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-3.41 32.00 2.38 15.00 0.85 0.80 0.06 0.99 0.03

COSMIC Results - P22557-1_143_578_6hrh.1.A.B

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-3.09 32.00 -1.50 11.00 0.54 0.49 0.02 1.00 0.01

Location of A282T in P22557-1_143_578_6hrh.1.A.B (NGL Viewer)

Variant Distributions

76 gnomAD38
46 clinvar
44 COSMIC

Ripley's Univariate K

gnomAD38
clinvar
COSMIC

Ripley's Bivariate D

clinvar - gnomAD38
COSMIC - gnomAD38

PathProx (clinvar - gnomAD38) Results

PathProx
PathProx clinvar ROC
PathProx clinvar PR

PathProx (COSMIC - gnomAD38) Results

PathProx
PathProx COSMIC ROC
PathProx COSMIC PR

GENSCAN00000017881_2.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 GENSCAN00000017881_2 A 5qr1 99.0 1.0 140 578 17.18 10.58 0.5 0.958 -0.01 0.471

clinvar Results - GENSCAN00000017881_2.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-2.15 38.00 2.67 33.00 0.97 0.96 0.50 0.87 0.30

COSMIC Results - GENSCAN00000017881_2.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-2.08 38.00 -1.09 8.00 0.49 0.47 -0.01 1.00 0.00

Location of A282T in GENSCAN00000017881_2.A (NGL Viewer)

Variant Distributions

38 gnomAD38
23 clinvar
22 COSMIC

Ripley's Univariate K

gnomAD38
clinvar
COSMIC

Ripley's Bivariate D

clinvar - gnomAD38
COSMIC - gnomAD38

PathProx (clinvar - gnomAD38) Results

PathProx
PathProx clinvar ROC
PathProx clinvar PR

PathProx (COSMIC - gnomAD38) Results

PathProx
PathProx COSMIC ROC
PathProx COSMIC PR

GENSCAN00000017881_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 GENSCAN00000017881_3 A 5txt 37.0 1.0 143 547 0.37 0.908 0.03 0.498

clinvar Results - GENSCAN00000017881_3.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
1.71 8.00 1.16 37.00 0.92 0.91 0.37 0.81 0.32

COSMIC Results - GENSCAN00000017881_3.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
1.72 8.00 -1.51 11.00 0.45 0.50 0.03 1.00 0.02

Location of A282T in GENSCAN00000017881_3.A (NGL Viewer)

Variant Distributions

33 gnomAD38
20 clinvar
22 COSMIC

Ripley's Univariate K

gnomAD38
clinvar
COSMIC

Ripley's Bivariate D

clinvar - gnomAD38
COSMIC - gnomAD38

PathProx (clinvar - gnomAD38) Results

PathProx
PathProx clinvar ROC
PathProx clinvar PR

PathProx (COSMIC - gnomAD38) Results

PathProx
PathProx COSMIC ROC
PathProx COSMIC PR

GENSCAN00000017881_4.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 GENSCAN00000017881_4 A 2bwn 50.0 1.0 144 540 2.66 2.81 0.29 0.889 -0.02 0.503

clinvar Results - GENSCAN00000017881_4.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-1.99 26.00 2.74 26.00 0.86 0.89 0.29 0.92 0.18

COSMIC Results - GENSCAN00000017881_4.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-1.87 26.00 -1.60 9.00 0.45 0.50 -0.02 1.00 0.00

Location of A282T in GENSCAN00000017881_4.A (NGL Viewer)

Variant Distributions

31 gnomAD38
20 clinvar
21 COSMIC

Ripley's Univariate K

gnomAD38
clinvar
COSMIC

Ripley's Bivariate D

clinvar - gnomAD38
COSMIC - gnomAD38

PathProx (clinvar - gnomAD38) Results

PathProx
PathProx clinvar ROC
PathProx clinvar PR

PathProx (COSMIC - gnomAD38) Results

PathProx
PathProx COSMIC ROC
PathProx COSMIC PR

AF-P22557-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-P22557-F1 A 0.0 1.0 83.95 96.67 1 587 0.42 3.61 0.31 0.835 -0.01 0.356

clinvar Results - AF-P22557-F1.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-2.47 27.00 5.20 26.00 0.89 0.84 0.31 0.96 0.14

COSMIC Results - AF-P22557-F1.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-2.47 27.00 -1.16 6.00 0.48 0.36 -0.01 1.00 0.00

Location of A282T in AF-P22557-F1.A (NGL Viewer)

Variant Distributions

65 gnomAD38
23 clinvar
29 COSMIC

Ripley's Univariate K

gnomAD38
clinvar
COSMIC

Ripley's Bivariate D

clinvar - gnomAD38
COSMIC - gnomAD38

PathProx (clinvar - gnomAD38) Results

PathProx
PathProx clinvar ROC
PathProx clinvar PR

PathProx (COSMIC - gnomAD38) Results

PathProx
PathProx COSMIC ROC
PathProx COSMIC PR

5qr1.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 5qr1 A 1.44 1.0 143 578 0.06 0.785 0.02 0.509

clinvar Results - 5qr1.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-3.68 36.00 1.89 15.00 0.83 0.78 0.06 0.99 0.03

COSMIC Results - 5qr1.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-3.33 32.00 -1.57 11.00 0.55 0.51 0.02 1.00 0.01

Location of A282T in 5qr1.A (NGL Viewer)

Variant Distributions

74 gnomAD38
46 clinvar
44 COSMIC

Ripley's Univariate K

gnomAD38
clinvar
COSMIC

Ripley's Bivariate D

clinvar - gnomAD38
COSMIC - gnomAD38

PathProx (clinvar - gnomAD38) Results

PathProx
PathProx clinvar ROC
PathProx clinvar PR

PathProx (COSMIC - gnomAD38) Results

PathProx
PathProx COSMIC ROC
PathProx COSMIC PR

5qr1.B 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 5qr1 B 1.44 1.0 143 578 23.53 9.62 0.49 0.954 0.03 0.528

clinvar Results - 5qr1.B

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-2.52 38.00 2.37 33.00 0.96 0.95 0.49 0.87 0.30

COSMIC Results - 5qr1.B

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-2.49 36.00 -1.16 12.00 0.59 0.53 0.03 1.00 0.02

Location of A282T in 5qr1.B (NGL Viewer)

Variant Distributions

37 gnomAD38
23 clinvar
22 COSMIC

Ripley's Univariate K

gnomAD38
clinvar
COSMIC

Ripley's Bivariate D

clinvar - gnomAD38
COSMIC - gnomAD38

PathProx (clinvar - gnomAD38) Results

PathProx
No graphic was created
PathProx clinvar ROC
PathProx clinvar PR

PathProx (COSMIC - gnomAD38) Results

PathProx
No graphic was created
PathProx COSMIC ROC
PathProx COSMIC PR