Home Structure Report ENSP00000374152.4_1 monomer AF-Q6GMV2-F1 monomer
Date 2024-01-02
Case SampleCase
Gene SMYD5
Protein Q6GMV2
Variant A57E

A57 Rate4Site Score ENST00000389501.9

Rate4Site Score QQ-Interval Std MSA
Normalized: 0.43 0.22, 0.73 0.48 90.00/100

A57 Cosmis Score Q6GMV2

Cosmis Score pValue cossyn source
Normalized: 0.16 0.67 -0.60 AF2

MusiteDeep (PTMs) within 8.0A of A57

PTM Residue PTM Type Probability
70 S-palmitoyl_cysteine 0.6
73 S-palmitoyl_cysteine 0.6
305 O-linked_glycosylation 0.6

ScanNet Prediction of A57 participation in a PPI

Binding Site Probability
0.0

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 ENSP00000374152.4_1 A 3qww 33.0 1.0 19 410 0.05 0.316
alphafold AF-Q6GMV2-F1 A 0.0 1.0 88.38 97.48 1 418 27.1 7.34 0.01 0.31

ENSP00000374152.4_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 ENSP00000374152.4_1 A 3qww 33.0 1.0 19 410 0.05 0.316

clinvar Results - ENSP00000374152.4_1.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-1.21 15.00 0.00 0.00 0.00 0.00 0.00 0.94 0.00

COSMIC Results - ENSP00000374152.4_1.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
-1.28 15.00 -1.61 10.00 0.36 0.32 0.05 0.98 0.04

Location of A57E in ENSP00000374152.4_1.A (NGL Viewer)

Variant Distributions

46 gnomAD38
clinvar
No clinvar Variants map to this structure
17 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

AF-Q6GMV2-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-Q6GMV2-F1 A 0.0 1.0 88.38 97.48 1 418 27.1 7.34 0.01 0.31

clinvar Results - AF-Q6GMV2-F1.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
1.98 37.00 0.00 0.00 0.00 0.00 0.00 0.95 0.00

COSMIC Results - AF-Q6GMV2-F1.A

Neutral Kz Neutral Kt Pathogenic Kz Pathogenic Kt ROC AUC PR AUC PathProx Neutral Constraint Pathogenic Constraint
1.78 37.00 -1.96 12.00 0.37 0.31 0.01 0.99 0.02

Location of A57E in AF-Q6GMV2-F1.A (NGL Viewer)

Variant Distributions

51 gnomAD38
clinvar
No clinvar Variants map to this structure
19 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