This report serves to summarize the functional impact of missense mutations in each gene as determined by Mutation Assessor[1].
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High Functional Impact Missense Mutations: 4534
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Medium Functional Impact Missense Mutations: 19281
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Low Functional Impact Missense Mutations: 18139
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Neutral Functional Impact Mutations: 12717
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 | 72 | 4 | 2 | 3.1450 | medium | medium |
| STK11 | 2 | 8 | 2 | 0 | 0 | 4.6175 | high | high |
| KEAP1 | 3 | 8 | 17 | 8 | 0 | 2.6150 | medium | medium |
| KRAS | 4 | 4 | 55 | 0 | 0 | 3.1350 | medium | medium |
| SMARCA4 | 5 | 2 | 1 | 2 | 2 | 1.8950 | low | high/low/neutral |
| ARID1A | 6 | 0 | 2 | 3 | 0 | 1.3200 | low | low |
| NF1 | 7 | 0 | 3 | 5 | 5 | 1.4300 | low | low/neutral |
| U2AF1 | 8 | 5 | 0 | 0 | 0 | 3.8200 | high | high |
| EGFR | 9 | 1 | 14 | 3 | 6 | 2.5950 | medium | medium |
| SETD2 | 10 | 2 | 1 | 4 | 4 | 1.6700 | low | low/neutral |
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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 LUAD-TP.maf.annotated. These are summarized in Table 1, sorted by MutSig rank.
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.