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: 2582

  • Medium Functional Impact Missense Mutations: 15081

  • Low Functional Impact Missense Mutations: 15391

  • Neutral Functional Impact Mutations: 10447

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 PIK3CA 0 56 131 150 1.2700 low neutral
2 TP53 0 167 3 3 3.1150 medium medium
3 GATA3 1 2 3 3 1.3900 low low/neutral
4 MAP3K1 4 1 9 2 1.6850 low low
5 CDH1 5 5 2 3 3.1550 medium high/medium
6 CBFB 0 8 2 0 2.3875 medium medium
7 PTEN 7 5 1 0 3.5750 high high
8 RUNX1 0 7 4 0 3.1250 medium medium
9 MLL3 3 8 11 6 1.6550 low low
11 MAP2K4 2 7 1 2 2.5375 medium medium
Methods & Data
Input

  1. BRCA-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 BRCA-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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