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: 1535

  • Medium Functional Impact Missense Mutations: 8897

  • Low Functional Impact Missense Mutations: 9018

  • Neutral Functional Impact Mutations: 6670

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
PTEN 1 6 2 0 0 3.9050 high high
MLL3 2 2 15 5 5 1.9950 medium medium
GIGYF2 4 0 0 1 0 1.0650 low low
PIK3CA 7 0 46 101 124 1.1400 low neutral
NCOA3 8 0 4 2 2 1.8875 low medium
RBMX 10 0 0 0 1 -0.9750 neutral neutral
RUNX1 11 0 6 1 0 3.1850 medium medium
PIK3R1 12 0 4 2 1 2.3400 medium medium
MEF2A 13 0 0 1 0 1.7650 low low
NCOR2 14 0 0 3 0 1.1800 low low
Methods & Data
Input

  1. BRCA-TP.maf.annotated

  2. BRCA-TP.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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