ETV6 - morinlab/LLMPP GitHub Wiki

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ETV6

Overview

ETV6 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. The prevalence of mutations in DLBCL has varied across different studies and may occur in as many as 10% of patients. This gene has some recurrent sites of mutations (hot spots) including multiple mutations predicted to affect splicing of ETV6 pre-mRNA. The mutation pattern in DLBCL mplies the preferential accumulation of inactivating mutations. Coding and non-coding mutations in this gene are associated with the MCD genetic subgroup of DLBCL.

History

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timeline
    title Publication timing
2012-03-06 : Lohr : DLBCL
2017-05-01 : Albuquerque : DLBCL
2017-10-10 : Reddy : DLBCL
2018-04-12 : Schmitz : DLBCL
2018-05-01 : Chapuy : DLBCL
2018-10-01 : Arthur : DLBCL

Relevance tier by entity

Entity	Tier	Description
	1	aSHM target and high-confidence DLBCL gene[@lohrDiscoveryPrioritizationSomatic2012a; @albuquerqueEnhancingKnowledgeDiscovery2017a; @reddyGeneticFunctionalDrivers2017]

Mutation incidence in large patient cohorts (GAMBL reanalysis)

Entity	source	frequency (%)
DLBCL	GAMBL genomes	4.97
DLBCL	Schmitz cohort	10.43
DLBCL	Reddy cohort	5.81
DLBCL	Chapuy cohort	10.26

Mutation pattern and selective pressure estimates

Entity	aSHM	Significant selection	dN/dS (missense)	dN/dS (nonsense)
BL	Yes	No	1.527	0.000
DLBCL	Yes	Yes	2.366	28.723
FL	Yes	No	2.772	0.000

aSHM regions

chr_name	hg19_start	hg19_end	region	regulatory_comment
chr12	11796001	11812968	TSS	strong_enhancer

ETV6 Hotspots

Chromosome	Coordinate (hg19)	ref>alt	HGVSp
chr12	11803078	C>T	A6V
chr12	11803087	G>A	S9N
chr12	11803094	G>A	K11=

View coding variants in ProteinPaint hg19 or hg38

View all variants in GenomePaint hg19 or hg38