HIST1H2AM - morinlab/LLMPP GitHub Wiki

HIST1H2AM

<<Warn("The variants reported in this gene in BL failed QC")>>

See below or the study page for more information

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.

History

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timeline
    title Publication timing
      2017-01-26 : Krysiak : FL
      2019-09-26 : Panea : BL

Relevance tier by entity

Entity Tier Description
DLBCL 1 high-confidence DLBCL gene
FL 1 high-confidence FL gene
BL 2-F Failed QC

Mutation incidence in large patient cohorts (GAMBL reanalysis)

Entity source frequency (%)
DLBCL GAMBL genomes 5.93
DLBCL Schmitz cohort 5.74
DLBCL Reddy cohort 4.80
DLBCL Chapuy cohort 5.98
FL GAMBL genomes 3.70
BL GAMBL genomes+capture 1.85
BL Thomas cohort 1.70
BL Panea cohort 3.00

Mutation pattern and selective pressure estimates

Entity aSHM Significant selection dN/dS (missense) dN/dS (nonsense)
DLBCL No No 1.844 0
FL No No 1.845 0
BL No No 2.149 0

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

View coding variants in ProteinPaint hg19 or hg38

View all variants in GenomePaint hg19 or hg38

Representative Mutations

BL2

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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;
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