Home Structure Report P22557-4_130_565_6hrh.1.A monomer P22557-4_130_565_6hrh.1.A trimer ENSP00000379501.3_2 monomer ENSP00000379501.3_3 monomer ENSP00000379501.3_4 monomer 5qqr dimer 5qqr monomer
Date 2024-01-02
Case SampleCase
Gene ALAS2
Protein P22557-4
Variant A269T

MusiteDeep (PTMs) within 8.0A of A269

PTM Residue PTM Type Probability
355 Methylarginine 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
swiss P22557-4_130_565_6hrh.1.A B 6hrh.1.A 99.78 1.0 130 565 22.93 10.41 0.46 0.966 0.03 0.527
swiss P22557-4_130_565_6hrh.1.A B 6hrh.1.A 99.78 1.0 130 565 0.06 0.797 0.02 0.494
modbase ENSP00000379501.3_2 A 5qr1 99.0 1.0 127 565 17.04 11.29 0.5 0.958 -0.01 0.471
modbase ENSP00000379501.3_3 A 5txt 37.0 1.0 130 534 0.37 0.908 0.03 0.498
modbase ENSP00000379501.3_4 A 2bwn 50.0 1.0 131 527 2.39 2.81 0.29 0.874 -0.02 0.479
X-RAY 5qqr A 1.46 1.0 130 565 0.0 0.784 0.07 0.507
X-RAY 5qqr B 1.46 1.0 130 565 23.86 8.74 0.23 0.954 0.14 0.53


P22557-4_130_565_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 P22557-4_130_565_6hrh.1.A B 6hrh.1.A 99.78 1.0 130 565 22.93 10.41 0.46 0.966 0.03 0.527

clinvar Results - P22557-4_130_565_6hrh.1.A.B

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-2.46 39.00 2.57 34.00 0.97 0.97 0.46 0.85 0.30

COSMIC Results - P22557-4_130_565_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 -1.07 11.00 0.55 0.53 0.03 1.00 0.02

Location of A269T in P22557-4_130_565_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


P22557-4_130_565_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 P22557-4_130_565_6hrh.1.A B 6hrh.1.A 99.78 1.0 130 565 0.06 0.797 0.02 0.494

clinvar Results - P22557-4_130_565_6hrh.1.A.B

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-3.39 32.00 2.38 15.00 0.85 0.80 0.06 0.99 0.03

COSMIC Results - P22557-4_130_565_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 A269T in P22557-4_130_565_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


ENSP00000379501.3_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 ENSP00000379501.3_2 A 5qr1 99.0 1.0 127 565 17.04 11.29 0.5 0.958 -0.01 0.471

clinvar Results - ENSP00000379501.3_2.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-2.14 38.00 2.67 33.00 0.97 0.96 0.50 0.87 0.30

COSMIC Results - ENSP00000379501.3_2.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-2.08 38.00 -1.10 8.00 0.49 0.47 -0.01 1.00 0.00

Location of A269T in ENSP00000379501.3_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


ENSP00000379501.3_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 ENSP00000379501.3_3 A 5txt 37.0 1.0 130 534 0.37 0.908 0.03 0.498

clinvar Results - ENSP00000379501.3_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 - ENSP00000379501.3_3.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
1.72 8.00 -1.49 11.00 0.45 0.50 0.03 1.00 0.02

Location of A269T in ENSP00000379501.3_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


ENSP00000379501.3_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 ENSP00000379501.3_4 A 2bwn 50.0 1.0 131 527 2.39 2.81 0.29 0.874 -0.02 0.479

clinvar Results - ENSP00000379501.3_4.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-1.97 25.00 2.51 26.00 0.86 0.87 0.29 0.92 0.18

COSMIC Results - ENSP00000379501.3_4.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-1.93 27.00 -1.61 9.00 0.44 0.48 -0.02 1.00 0.00

Location of A269T in ENSP00000379501.3_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


5qqr.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 5qqr A 1.46 1.0 130 565 0.0 0.784 0.07 0.507

clinvar Results - 5qqr.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-3.70 36.00 1.97 15.00 0.83 0.78 0.00 0.98 0.02

COSMIC Results - 5qqr.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-3.33 34.00 -1.58 11.00 0.53 0.51 0.07 1.00 0.02

Location of A269T in 5qqr.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


5qqr.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 5qqr B 1.46 1.0 130 565 23.86 8.74 0.23 0.954 0.14 0.53

clinvar Results - 5qqr.B

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-2.55 38.00 2.39 33.00 0.96 0.95 0.23 0.89 0.19

COSMIC Results - 5qqr.B

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-2.48 36.00 -1.20 11.00 0.54 0.53 0.14 1.00 0.05

Location of A269T in 5qqr.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