Mutation Assessor
Overview
Introduction

This report serves to summarize the functional impact of missense mutations in each gene as determined by Mutation Assessor[1].

Summary

  • High Functional Impact Missense Mutations: 811

  • Medium Functional Impact Missense Mutations: 4211

  • Low Functional Impact Missense Mutations: 3844

  • Neutral Functional Impact Mutations: 3023

Results
Functional Impact by Gene

Table 1.  Get Full Table A gene-level breakdown of missense mutation functional impact, ordered by MutSig rank. Includes missense mutation counts broken down by level of functional impact (high, medium, low, neutral), median functional impact score and level, and most common level(s) of functional impact (mode) per gene.

MutSig
Rank 		Gene High
Functional Impact
Count 		Medium
Functional Impact
Count 		Low
Functional Impact
Count 		Neutral
Functional Impact
Count 		Median
Functional Impact
Score 		Median
Functional Impact
Level 		Mode
Functional Impact
Level
1 TP53 0 75 2 0 3.0750 medium medium
2 PIK3R1 1 12 1 0 2.7100 medium medium
4 NF1 0 3 0 1 2.3950 medium medium
5 PTEN 16 24 5 0 2.9600 medium medium
6 IDH1 14 0 0 0 4.5400 high high
7 PIK3CA 0 12 7 4 1.9650 medium medium
9 SLC26A3 0 1 2 3 1.0050 low neutral
10 SEMG1 0 1 4 2 1.6100 low low
11 KDR 0 1 3 2 1.2075 low low
12 RPL5 2 0 0 0 3.9350 high high
Methods & Data
Input

  1. GBM-TP.maf.annotated

  2. sig_genes.txt

  3. Mutation Assessor Scores Release 2:

A lookup is done against the relevant Mutation Assessor Scores table for each missense mutation in a given MAF file, and available functional impact score and level are appended as two new columns to generate GBM-TP.maf.annotated. These are summarized in Table 1, sorted by MutSig rank.

References
[1] Boris Reva, Yevgeniy Antipin, and Chris Sander, Predicting the functional impact of protein mutations: application to cancer genomics, Nucl. Acids Res. 39(17):e118 (2011)
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