Mutation Assessor
Kidney Chromophobe (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
Maintained by David Heiman (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Mutation Assessor. Broad Institute of MIT and Harvard. doi:10.7908/C1W66JJ8
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: 168

  • Medium Functional Impact Missense Mutations: 1078

  • Low Functional Impact Missense Mutations: 1105

  • Neutral Functional Impact Mutations: 1214

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
TP53 1 0 15 2 0 3.0200 medium medium
PTEN 2 0 0 2 0 1.4550 low low
PABPC1 3 0 2 2 0 1.4400 low medium/low
URGCP 4 0 1 0 0 2.6750 medium medium
FAM26F 5 0 2 0 0 2.2875 medium medium
PABPC3 6 0 3 2 4 1.0500 low neutral
RNF145 7 0 0 0 3 0.0000 neutral neutral
GFM1 8 0 0 0 1 0.0000 neutral neutral
RIPPLY2 9 0 1 0 0 2.5700 medium medium
MUC16 10 0 2 6 5 1.0400 low low
Methods & Data
Input
  1. KICH-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 KICH-TP.maf.annotated. These are summarized in Table 1, sorted by MutSig rank.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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)