Home Structure Report Q9NZ71-1_3_756_7o75.1.A monomer ENSP00000359035.3_2 monomer ENSP00000359035.3_1 monomer ENSP00000359035.3_3 monomer AF-Q9NZ71-F1 monomer
Date 2024-01-02
Case SampleCase
Gene RTEL1
Protein Q9NZ71-1
Variant G546D

G546 Cosmis Score Q9NZ71-1

Cosmis Score pValue cossyn source
Normalized: -0.64 0.33 0.24 SWISS-MODEL

MusiteDeep (PTMs) within 8.0A of G546

PTM Residue PTM Type Probability
543 Ubiquitination 0.6
586 N6-acetyllysine 0.6

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 Q9NZ71-1_3_756_7o75.1.A A 7o75.1.A 26.52 1.0 3 756 0.16 0.519 -0.03 0.598
modbase ENSP00000359035.3_2 A 3crv 30.0 1.0 21 747 0.46 0.582 -0.02 0.243
modbase ENSP00000359035.3_1 A 4a15 20.0 1.0 21 715 0.46 0.263 -0.02 0.269
modbase ENSP00000359035.3_3 A 6fwr 21.0 1.0 204 714 0.0 0.341 0.12 0.443
alphafold AF-Q9NZ71-F1 A 0.0 1.0 72.71 94.64 1 1219 2.03 0.12 0.06 0.385 0.01 0.301


Q9NZ71-1_3_756_7o75.1.A.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
swiss Q9NZ71-1_3_756_7o75.1.A A 7o75.1.A 26.52 1.0 3 756 0.16 0.519 -0.03 0.598

clinvar Results - Q9NZ71-1_3_756_7o75.1.A.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
2.25 5.00 1.42 13.00 0.72 0.52 0.16 0.99 0.06

COSMIC Results - Q9NZ71-1_3_756_7o75.1.A.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
1.86 10.00 0.82 20.00 0.75 0.60 -0.03 0.98 0.01

Location of G546D in Q9NZ71-1_3_756_7o75.1.A.A (NGL Viewer)

Variant Distributions

110 gnomAD38
11 clinvar
26 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


ENSP00000359035.3_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 ENSP00000359035.3_2 A 3crv 30.0 1.0 21 747 0.46 0.582 -0.02 0.243

clinvar Results - ENSP00000359035.3_2.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
2.16 8.00 1.43 23.00 0.72 0.58 0.46 0.97 0.19

COSMIC Results - ENSP00000359035.3_2.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
2.10 9.00 -1.87 12.00 0.41 0.24 -0.02 0.99 0.00

Location of G546D in ENSP00000359035.3_2.A (NGL Viewer)

Variant Distributions

107 gnomAD38
9 clinvar
26 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


ENSP00000359035.3_1.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 ENSP00000359035.3_1 A 4a15 20.0 1.0 21 715 0.46 0.263 -0.02 0.269

clinvar Results - ENSP00000359035.3_1.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
2.27 15.00 -1.05 41.00 0.61 0.26 0.46 0.90 0.25

COSMIC Results - ENSP00000359035.3_1.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
1.78 15.00 -1.81 12.00 0.42 0.27 -0.02 0.99 0.00

Location of G546D in ENSP00000359035.3_1.A (NGL Viewer)

Variant Distributions

103 gnomAD38
8 clinvar
24 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


ENSP00000359035.3_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 ENSP00000359035.3_3 A 6fwr 21.0 1.0 204 714 0.0 0.341 0.12 0.443

clinvar Results - ENSP00000359035.3_3.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
2.18 45.00 3.11 5.00 0.64 0.34 0.00 1.00 0.00

COSMIC Results - ENSP00000359035.3_3.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
1.90 45.00 -1.32 45.00 0.65 0.44 0.12 0.87 0.17

Location of G546D in ENSP00000359035.3_3.A (NGL Viewer)

Variant Distributions

85 gnomAD38
7 clinvar
14 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-Q9NZ71-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-Q9NZ71-F1 A 0.0 1.0 72.71 94.64 1 1219 2.03 0.12 0.06 0.385 0.01 0.301

clinvar Results - AF-Q9NZ71-F1.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-3.46 45.00 1.68 12.00 0.70 0.38 0.06 1.00 0.02

COSMIC Results - AF-Q9NZ71-F1.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-3.33 45.00 -1.23 15.00 0.57 0.30 0.01 1.00 0.01

Location of G546D in AF-Q9NZ71-F1.A (NGL Viewer)

Variant Distributions

259 gnomAD38
16 clinvar
43 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