S1PR2 - morinlab/LLMPP GitHub Wiki

bibliography: 'morinlab.bib' csl: 'NLM.csl' link-citations: true

S1PR2

Overview

S1PR2 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.

History

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timeline
    title Publication timing
2011-07-27 : Morin : DLBCL
2012-03-06 : Lohr : DLBCL
2013-08-15 : Morin : DLBCL
2014-12-11 : Muppidi : BL
2017-10-10 : Reddy : DLBCL
2018-04-12 : Schmitz : DLBCL
2018-10-01 : Arthur : DLBCL

Relevance tier by entity

Entity	Tier	Description
	1	high-confidence PMBL/cHL/GZL gene
	2	aSHM target; Although recurrent, the relevance of mutations in BL is tenuous [@muppidiLossSignalingGa132014b]
	1	aSHM target and high-confidence DLBCL gene [@morinFrequentMutationHistonemodifying2011; @lohrDiscoveryPrioritizationSomatic2012a; @morinMutationalStructuralAnalysis2013]
	1	aSHM target and high-confidence FL gene

Mutation incidence in large patient cohorts (GAMBL reanalysis)

Entity	source	frequency (%)
BL	GAMBL genomes+capture	1.15
BL	Thomas cohort	0.00
BL	Panea cohort	4.00
DLBCL	GAMBL genomes	4.78
DLBCL	Schmitz cohort	2.13
DLBCL	Reddy cohort	2.20
DLBCL	Chapuy cohort	2.56
FL	GAMBL genomes	6.24

Mutation pattern and selective pressure estimates

Entity	aSHM	Significant selection	dN/dS (missense)	dN/dS (nonsense)
BL	Yes	No	0.000	0.000
DLBCL	Yes	Yes	34.147	0.000
FL	Yes	Yes	36.780	339.679

aSHM regions

chr_name	hg19_start	hg19_end	region	regulatory_comment
chr19	10340142	10341764	TSS	active_promoter

View coding variants in ProteinPaint hg19 or hg38

View all variants in GenomePaint hg19 or hg38