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: 2569

  • Medium Functional Impact Missense Mutations: 12801

  • Low Functional Impact Missense Mutations: 13149

  • Neutral Functional Impact Mutations: 9085

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 92 2 0 3.1450 medium medium
2 CDKN2A 1 0 6 1 0.8950 low low
3 NFE2L2 0 27 0 0 2.8650 medium medium
4 MLL2 0 6 4 11 0.5500 neutral neutral
5 KEAP1 6 9 5 2 2.2500 medium medium
6 PTEN 6 2 0 0 3.7775 high high
7 PIK3CA 0 6 18 4 1.6200 low low
8 RB1 0 1 1 0 1.6825 low medium/low
9 CYP11B1 1 3 6 5 1.8450 low low
10 NOTCH1 2 3 0 3 2.4275 medium medium/neutral
Methods & Data
Input

  1. LUSC-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 LUSC-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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