Table of Contents

Overview

EBF1 is a critical transcription factor in early B-cell development, regulating the expression of key genes involved in B-cell differentiation, survival, and function. EBF1 is essential for proper B-cell receptor (BCR) signaling.1 Mutations in EBF1 can impair BCR signaling pathways, affecting B-cell survival and proliferation.1 EBF1 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. This gene has some recurrent sites of mutations (hot spots) but the mutation pattern in DLBCL and FL implies the preferential accumulation of inactivating mutations.

Experimental Evidence

Driver mutations affecting this gene in DLBCL/FL have been experimentally demonstrated to cause a reduction or loss of function (LOF).2

Relevance tier by entity

Entity Tier Description
BL 2 Role of EBF1 mutations in BL requires confirmation
DLBCL 1 High-confidence DLBCL gene
FL 1 High-confidence FL gene
PMBL 1 High-confidence PMBL gene

Mutation incidence in large patient cohorts (GAMBL reanalysis)

DLBCL

Entity Collection N mutated Incidence 95% CI
DLBCL GAMBL without Reddy 1,089 112 0.1028 [0.0848,0.1209]
DLBCL GAMBL with Reddy 2,088 200 0.0958 [0.0832,0.1084]
DLBCL BC 231 16 0.0693 [0.0365,0.102]
DLBCL Dana-Farber 303 38 0.1254 [0.0881,0.1627]
DLBCL NCI 470 51 0.1085 [0.0804,0.1366]
DLBCL Reddy 999 88 0.0881 [0.0705,0.1057]
DLBCL DLBCL_ICGC 85 7 0.0824 [0.0239,0.1408]

FL

pathology Collection N mutated Incidence CI
FL GAMBL without Crouch 642 51 0.0794 [0.0585,0.1004]
FL GAMBL with Crouch 1,189 122 0.1026 [0.0854,0.1199]
FL BC 379 30 0.0792 [0.052,0.1063]
FL Kalmbach 164 14 0.0854 [0.0426,0.1281]
FL Crouch 547 71 0.1298 [0.1016,0.158]
FL FL_ICGC 99 7 0.0707 [0.0202,0.1212]

Mutation pattern and selective pressure estimates

Entity Missense dN/dS Nonsense dN/dS Q value
BL 1.8082 0.0000 1
FL 12.4715 67.0333 0
DLBCL 3.0156 14.7320 0

aSHM regions

chr_name hg19_start hg19_end region regulatory_comment
chr5 158500476 158532769 TSS active_promoter

EBF1 Hotspots

Chromosome Coordinate (hg19) ref>alt HGVSp
chr5 158526467 C>T S7N
chr5 158526456 T>C S11G
chr5 158526413 T>C N25S
chr5 158511720 T>C N147D
chr5 158511714 C>T E149K
chr5 158511705 G>C R152G
chr5 158511698 A>C L154W
chr5 158511677 C>A C161F
chr5 158500470 C>T R163H
chr5 158500468 A>G C164R
chr5 158500467 C>G C164S

Visualizations

Protein

View coding variants in ProteinPaint hg19 or hg38

Genome

View all variants in GenomePaint hg19 or hg38

Expression

History

%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% timeline title Publication timing 2012-10-01 : Bohle : DLBCL 2013-08-15 : Morin : DLBCL 2015-02-12 : Reichel : PMBL 2017-05-01 : Albuquerque : DLBCL 2017-10-10 : Reddy : DLBCL 2018-05-01 : Chapuy : DLBCL 2018-10-01 : Arthur : DLBCL 2021-05-05 : Hubschmann : DLBCL

References

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2.
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Citing

If you use the information or data from this site, please cite

Krysta Coyle, Kostiantyn Dreval, Daniel Hodson and Ryan D. Morin. Audit of B-cell cancer genes. Blood Adv (2025) 9 (8): 2019–2031.

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