VarMod
Variant Modeller

Modelling functional effects of non-synonymous variants


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Submission Details
Email: mark@wass.com
Unique Submission identifier: vm53679d298872d
Description: Example
Uniprot Accession: P24941
Query Seq: MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVI
HTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGA
IKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEID
QLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAA
LAHPFFQDVTKPVPHLRL


Analysis Summary
The table below shows the machine learning VarMod prediction and a summary of the features used to make the predictionThey are colour coded to indicate how relevant each feature is likely to be when considering if the variant affects the protein functionThe sections below provide detailed information relating to sequence conservation, ligand binding sites and protein-protein interactions.The structural data can be used to investigate the structural environment of the variants and consider how this mayhave an effect on protein function.
VariantVarMod ProbabilityInterfaceBinding siteConservationsizeChargeFunc grp
E2V0.4560.2350.3360.294
A31P0.7870.1920.0000.714
F90T0.5630.1630.2120.643
T160R0.7560.0000.1270.773
Y180G0.6260.0000.5350.636


Sequence View - Conservation Data
1102030405060
SequenceMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNH
Conservation
Binding site
Interface
Variants
61708090100110120
SequencePNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHS
Conservation
Binding site
Interface
Variants
121130140150160170180
SequenceHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYY
Conservation
Binding site
Interface
Variants
181190200210220230240
SequenceSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSF
Conservation
Binding site
Interface
Variants
241250260270280290
SequencePKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Conservation
Binding site
Interface
Variants


Structural Analysis

Structural Templates

The details of the models generated for the protein are listed below.These include the structural templates used, the range of the protein sequence includedand the variants present within each of the models
ModelTemplateSequence RangeTemplate probabilityVariants present
14ek4_A 1-298 100Y180G, F90T, T160R, A31P, E2VDownload model
In this section view the structural model and the ligand binding and interface sites.The jmol viewer displays the model of the protein with these regions mapped onto the structure. The control panel on the right can be used to modify the display of the protein, and the residues - variants, binding sites and interfaces

Structural Model


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Display Controls

Protein Model

Variants

Predicted Binding Site Residues

Protein-Protein interface Residues

View


Interaction Data

Below is a list interaction partners in uniprot with the query protein. Models of the complex of these interactions are available.Click the relevant identifier to view the model in relation to the variants. They will be displayed in a separate window
P78396P24864O95067P24385
P24941P50613P38936Q99741
Q96Q40P20248O96020P14635
P30279P61024P46527Q16667