CDKN2A - morinlab/LLMPP GitHub Wiki
bibliography: 'morinlab.bib' csl: 'NLM.csl' link-citations: true nocite: | @spinaGeneticsNodalMarginal2016, @grandeGenomewideDiscoverySomatic2019, @morinMutationalStructuralAnalysis2013,
Overview
Although CDKN2A aberrations are common in DLBCL, this gene is predominantly affected by copy number alterations. One study found that deletions of the CDKN2A locus occur in about one-third of DLBCL patients.[@spinaGeneticsNodalMarginal2016] The mutation pattern in DLBCL and FL implies the preferential accumulation of inactivating mutations. This gene has some recurrent sites of mutations (hotspots) with the most common mutation causing a truncation at codon 80 (R80*).
Experimental Evidence
Driver mutations affecting this gene in DLBCL have been experimentally demonstrated to cause a reduction or loss of function (LOF).[@kannengiesserFunctionalStructuralGenetic2009]
Relevance tier by entity
include:tables/table1_CDKN2A.md
Mutation incidence in large patient cohorts (GAMBL reanalysis)
DLBCL
include:tables/DLBCL_CDKN2A.md
Mutation pattern and selective pressure estimates
| Entity | Isoform | aSHM | Significant selection | dN/dS (missense) | dN/dS (nonsense) |
|---|---|---|---|---|---|
| BL | CDKN2A.p14arf | No | No | 10.947 | 72.708 |
| DLBCL | CDKN2A.p14arf | No | Yes | 19.055 | 102.121 |
| FL | CDKN2A.p14arf | No | No | 0.000 | 117.964 |
| BL | CDKN2A.p16INK4a | No | No | 2.931 | 104.823 |
| DLBCL | CDKN2A.p16INK4a | No | Yes | 5.631 | 442.466 |
| FL | CDKN2A.p16INK4a | No | No | 0.000 | 159.196 |
CDKN2A Hotspots
| Chromosome | Coordinate (hg19) | ref>alt | HGVSp |
|---|---|---|---|
| chr9 | 21971120 | G>A | R80* |
include:tables/browser_CDKN2A.md
Expression
include:tables/mermaid_CDKN2A.md