CDKN2A - morinlab/LLMPP GitHub Wiki


bibliography: 'morinlab.bib' csl: 'NLM.csl' link-citations: true nocite: | @spinaGeneticsNodalMarginal2016, @grandeGenomewideDiscoverySomatic2019, @morinMutationalStructuralAnalysis2013,

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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

References