CXCR4 - morinlab/LLMPP GitHub Wiki


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CXCR4

Overview

CXCR4 is one of a number of genes affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus. No notable hot spots have been described in this gene in the context of the cancers listed below. The mutation pattern in DLBCL implies the preferential accumulation of inactivating mutations.

History

Mutations in this gene were first described in DLBCL in 2012 by Khodabakhshi et al,1 in FL in 2021 by Hübschmann et al2 and in BL in 2019 by Panea et al.3

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timeline
    title Publication timing
      2012-11-12 : Khodabakhshi : DLBCL
2017-01-26 : Krysiak : FL
2017-10-10 : Reddy : DLBCL
2018-05-01 : Chapuy : DLBCL
      2019-09-26 : Panea : BL
2021-05-05 : Hubschmann : DLBCL
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Relevance tier by entity

Entity Tier Description
MZL 1 high-confidence MZL gene
DLBCL 1 aSHM target and high-confidence DLBCL gene [@khodabakhshiRecurrentTargetsAberrant2012]
FL 2 aSHM target; Although recurrent, the relevance of mutations in FL is tenuous [@krysiakRecurrentSomaticMutations2017b]
BL 2 aSHM target; Although recurrent, the relevance of mutations in BL is tenuous [@paneaWholeGenomeLandscape2019]

Mutation incidence in large patient cohorts (GAMBL reanalysis)

Entity source frequency (%)
BL GAMBL genomes+capture 2.08
BL Thomas cohort 2.10
BL Panea cohort 2.00
DLBCL GAMBL genomes 2.87
DLBCL Schmitz cohort 2.55
DLBCL Reddy cohort 1.50
DLBCL Chapuy cohort 2.56
FL GAMBL genomes 3.46

Mutation pattern and selective pressure estimates

Entity aSHM Significant selection dN/dS (missense) dN/dS (nonsense)
BL Yes No 4.603 0.000
DLBCL Yes No 3.731 18.727
FL Yes No 0.000 0.000

aSHM regions

chr_name hg19_start hg19_end region regulatory_comment
chr2 136874728 136875461 intron weak_promoter

View coding variants in ProteinPaint hg19 or hg38

View all variants in GenomePaint hg19 or hg38

CXCR4 Expression

Representative Mutations

BL

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References

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