MYC - morinlab/LLMPP GitHub Wiki
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MYC
Overview
MYC 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
1992-12-01 : Johnston : BL
2001-07-19 : Pasqualucci : DLBCL
2017-07-27 : Jallades : MZL
2021-07-15 : Duns : PMBL
Relevance tier by entity
| Entity | Tier | Description |
|---|---|---|
 |
2 | relevance in PMBL/cHL/GZL not firmly established[@dunsCharacterizationDLBCLPMBL2021b] |
 |
2 | relevance in MZL not firmly established[@jalladesExomeSequencingIdentifies2017] |
 |
1-a | aSHM target and high-confidence BL gene [@johnstonCmycHypermutationBurkitt1992] |
 |
1-a | aSHM target and high-confidence DLBCL gene [@pasqualucciHypermutationMultipleProtooncogenes2001a] |
 |
2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous |
Mutation incidence in large patient cohorts (GAMBL reanalysis)
| Entity | source | frequency (%) |
|---|---|---|
| BL | GAMBL genomes+capture | 61.89 |
| BL | Thomas cohort | 60.20 |
| BL | Panea cohort | 49.50 |
| DLBCL | GAMBL genomes | 10.90 |
| DLBCL | Schmitz cohort | 5.32 |
| DLBCL | Reddy cohort | 6.21 |
| DLBCL | Chapuy cohort | 6.41 |
| FL | GAMBL genomes | 0.92 |
Mutation pattern and selective pressure estimates
| Entity | aSHM | Significant selection | dN/dS (missense) | dN/dS (nonsense) |
|---|---|---|---|---|
| BL | Yes | Yes | 7.754 | 3.964 |
| DLBCL | Yes | Yes | 2.850 | 2.582 |
| FL | Yes | No | 4.998 | 0.000 |
aSHM regions
| chr_name | hg19_start | hg19_end | region | regulatory_comment |
|---|---|---|---|---|
| chr8 | 128748352 | 128749427 | TSS | active_promoter |
MYC Hotspots
| Chromosome | Coordinate (hg19) | ref>alt | HGVSp |
|---|---|---|---|
| chr8 | 128750677 | C>A | P72T |
| chr8 | 128750677 | C>G | P72A |
| chr8 | 128750677 | C>T | P72S |
| chr8 | 128750677 | CC>TT | P72F |
| chr8 | 128750678 | C>G | P72R |
| chr8 | 128750678 | C>T | P72L |
| chr8 | 128750680 | A>G | T73A |
| chr8 | 128750681 | C>A | T73N |
| chr8 | 128750681 | C>T | T73I |
| chr8 | 128750681 | CC>AT | T73N |
| chr8 | 128750681 | CC>GT | T73S |
| chr8 | 128750681 | CC>TA | T73I |
| chr8 | 128750681 | CC>TG | T73M |
| chr8 | 128750681 | CC>TT | T73I |
| chr8 | 128750683 | C>G | P74A |
| chr8 | 128750683 | C>T | P74S |
| chr8 | 128750684 | C>T | P74L |
| chr8 | 128750686 | C>A | P75T |
| chr8 | 128750686 | C>G | P75A |
| chr8 | 128750686 | C>T | P75S |
| chr8 | 128750686 | CC>TT | P75F |
| chr8 | 128750687 | C>A | P75H |
| chr8 | 128750687 | C>G | P75R |
| chr8 | 128750692 | T>C | S77P |
| chr8 | 128750692 | T>G | S77A |
| chr8 | 128750693 | C>G | S77C |
| chr8 | 128750695 | C>T | P78S |
| chr8 | 128750696 | C>G | P78R |
View coding variants in ProteinPaint hg19 or hg38
View all variants in GenomePaint hg19 or hg38
MYC Expression
