Table of Contents

Overview

This gene encodes the H2A protein, one of the core proteins comprising nucleosomes. Although relatively common in DLBCL, little is known about the function of these mutations. The relevance of HIST1H2AM mutations in DLBCL remains unclear. Selective pressure analysis did not identify this gene as significantly enriched for either missense or truncating mutations, indicating that many of these mutations may represent passengers.

Relevance tier by entity

Entity Tier Description
BL 3 Mutations are unlikely to be relevant to BL
DLBCL 1 High-confidence DLBCL gene
FL 1 High-confidence FL gene

Warnings

The variants reported in this gene in BL failed QC

See below or the study page for more information

Mutation incidence in large patient cohorts (GAMBL reanalysis)

DLBCL

Entity Collection N mutated Incidence 95% CI
DLBCL GAMBL without Reddy 1,089 63 0.0579 [0.044,0.0717]
DLBCL GAMBL with Reddy 2,088 111 0.0532 [0.0435,0.0628]
DLBCL BC 231 9 0.0390 [0.014,0.0639]
DLBCL Dana-Farber 303 19 0.0627 [0.0354,0.09]
DLBCL NCI 470 27 0.0574 [0.0364,0.0785]
DLBCL Reddy 999 48 0.0480 [0.0348,0.0613]
DLBCL DLBCL_ICGC 85 8 0.0941 [0.032,0.1562]

BL

pathology Collection N mutated Incidence CI
BL GAMBL without Panea 309 5 0.0154 [0.0017,0.0291]
BL GAMBL without ICGC/Zhou 320 7 0.0208 [0.0052,0.0364]
BL GAMBL with Panea 410 8 0.0175 [0.0048,0.0302]
BL BLGSP 219 4 0.0183 [5e-04,0.036]
BL Zhou/ICGC 90 1 0.0111 [0,0.0328]
BL Panea 101 3 0.0297 [0,0.0628]

FL

pathology Collection N mutated Incidence CI
FL GAMBL without Crouch 642 19 0.0296 [0.0165,0.0427]
FL GAMBL with Crouch 1,189 39 0.0328 [0.0227,0.0429]
FL BC 379 15 0.0396 [0.0199,0.0592]
FL Kalmbach 164 4 0.0244 [8e-04,0.048]
FL Crouch 547 20 0.0366 [0.0208,0.0523]
FL FL_ICGC 99 0 0.0010 [0,0.0073]

Mutation pattern and selective pressure estimates

Entity Missense dN/dS Nonsense dN/dS Q value
BL 3.1445 0.0000 1.0000
FL 2.4531 0.0000 1.0000
DLBCL 0.8527 1.2576 0.2353

HIST1H2AM Hotspots

Chromosome Coordinate (hg19) ref>alt HGVSp
chr6 27860660 T>C N90D
chr6 27860658 G>C N90K
chr6 27860652 C>G E92D
chr6 27860652 C>A E92D
chr6 27860649 C>G E93D
chr6 27860648 G>C L94V
chr6 27860648 G>A L94F
chr6 27860644 T>C N95S
chr6 27860643 G>C N95K
chr6 27860640 C>G K96N
chr6 27860640 C>A K96N
chr6 27860639 G>C L97V
chr6 27860636 G>C L98V
chr6 27860636 G>A L98F
chr6 27860633 C>G G99R
chr6 27860632 C>G G99A
chr6 27860627 C>G V101L
chr6 27860627 C>T V101I
chr6 27860627 C>A V101F
chr6 27860624 T>A T102S
chr6 27860623 G>C T102S
chr6 27860623 G>A T102I
chr6 27860560 C>G S123T
chr6 27860559 G>C S123R
chr6 27860549 C>G A127P
chr6 27860548 G>C A127G
chr6 27860548 G>A A127V
chr6 27860542 C>T G129D
chr6 27860538 C>G K130N

Visualizations

Protein

View coding variants in ProteinPaint hg19 or hg38

Genome

View all variants in GenomePaint hg19 or hg38

Representative Mutations

BL2

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History

%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%% timeline title Publication timing 2017-01-26 : Krysiak : FL 2019-09-26 : Panea : BL

References

1.
Krysiak K, Gomez F, White BS, Matlock M, Miller CA, Trani L, Fronick CC, Fulton RS, Kreisel F, Cashen AF, Carson KR, Berrien-Elliott MM, Bartlett NL, Griffith M, Griffith OL, Fehniger TA. Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma. Blood. 2017 Jan 26;129(4):473–483. PMCID: PMC5270390
2.
Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019;

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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