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: 1798

  • Medium Functional Impact Missense Mutations: 7761

  • Low Functional Impact Missense Mutations: 7218

  • Neutral Functional Impact Mutations: 5288

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.

Gene MutSig
Rank 		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
IDH1 1 398 0 0 0 4.540 high high
TP53 2 0 244 2 1 3.145 medium medium
CIC 4 16 29 17 4 3.320 medium medium
NOTCH1 5 10 10 0 5 3.155 medium high/medium
EGFR 6 7 31 4 1 2.990 medium medium
PIK3R1 7 0 6 1 0 2.710 medium medium
IDH2 8 20 0 0 0 3.900 high high
NF1 9 0 7 2 2 2.250 medium medium
PTEN 10 7 6 2 0 3.460 medium high
FUBP1 11 0 0 0 1 0.705 neutral neutral
Methods & Data
Input

  1. LGG-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 LGG-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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