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MYD88
Final classification
Pathogenic
MYD88 c.818T>C · p.Leu273Pro
MYD88

MYD88 c.818T>C (p.Leu273Pro), corresponding to the canonical L265P mutation, is a well-characterized gain-of-function missense variant in the TIR domain BB-loop (PM1_moderate).

Gene
MYD88
Transcript
NM_001172567.1
HGVS · transcript:coding
NM_001172567.1:c.818T>C
Consequence
N/A
GRCh38
chr3:38141150 T>C
GRCh37
chr3:38182641 T>C
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PS3 strong, PS4 strong, PM1 moderate, PM2 supporting, PP3 supporting; combination = 2 strong + 1 moderate + 2 supporting, which maps to Pathogenic.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PS3 strong, PS4 strong, PM1 moderate, PM2 supporting, PP3 supporting; combination = 2 strong + 1 moderate + 2 supporting, which maps to Pathogenic.
Classification rationale
PS3PS4PM1PM2PP3 Pathogenic
MYD88 c.818T>C

MYD88 c.818T>C (p.Leu273Pro), corresponding to the canonical L265P mutation, is a well-characterized gain-of-function missense variant in the TIR domain BB-loop (PM1_moderate).1 Multiple independent functional studies demonstrate that this variant constitutively activates NF-kappaB and JAK/STAT signaling, confers cytokine-independent survival, and that mutant-specific knockdown or pharmacologic inhibition is selectively toxic to MYD88-mutant cells (PS3_strong).2 The variant is highly enriched in affected individuals, detected in approximately 90% of Waldenstrom macroglobulinemia cases and recurrent in ABC DLBCL and IgM-MGUS, compared to an extremely low population frequency of 0.0026-0.0052% in gnomAD with zero homozygotes (PS4_strong).3 The variant is absent or extremely rare in population databases, with gnomAD v2.1 AF=5.17e-05 and v4.1 AF=2.60e-05, both well below the 0.1% threshold (PM2_supporting).4 In silico predictors support a deleterious effect: REVEL score of 0.735 exceeds the pathogenicity threshold of 0.5, though BayesDel (0.13148) is borderline and SpliceAI predicts no splicing impact (PP3_supporting).5 All benign criteria were assessed and none were met. BS3 is specifically contradicted by well-established functional evidence of a gain-of-function damaging effect. BA1 and BS1 are not met as population frequencies remain well below benign thresholds.6 Applying generic ACMG/AMP 2015 combination rules: 2 Strong (PS3, PS4) + 1 Moderate (PM1) + 2 Supporting (PM2, PP3) meets the threshold for Pathogenic (>=2 Strong).7 CAVEAT: The evidence supporting PS3_strong and PS4_strong derives predominantly from somatic tumor studies. The variant is almost exclusively observed as a somatic mutation in hematologic malignancies. The germline ACMG/AMP framework is being applied to a variant with a somatic disease mechanism. Classification should be interpreted with this context, and human review is recommended to confirm the appropriateness of this germline-classification for the clinical indication.

PS3 + PS4 + PM1 + PM2 + PP3 Pathogenic
Gene diagram · NM_001172567.1 · variants mapped to exon structure
MYD88 NM_001172567.1
Fetching transcript structure from UCSC…
Applied criteria · 5 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency · supports pathogenic
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      Population frequency
      Overall AF
      42 / 1,614,060
      0.0026%
      Highest · Ashkenazi Jewish
      0.01%
      Homozygotes
      0
      grpmax FAF
      0.0021%
      Allele frequency by ancestry — gnomAD v4.1
      observed in 5 of 9 groups
      AncestryAllele countFrequencyHomozygotes
      Ashkenazi Jewish 3 / 29,600 0.01% 0
      Admixed American 2 / 60,016 0.0033% 0
      European (non-Finnish) 34 / 1,179,918 0.0029% 0
      East Asian 1 / 44,870 0.0022% 0
      South Asian 1 / 91,084 0.0011% 0
      European (Finnish) 0 / 64,034
      Amish 0 / 912
      Middle Eastern 0 / 6,062
      African/African American 0 / 75,056
      This variant is present in gnomAD v4.1 (AF= 2.60213e-05; MAF= 0.00260%, 42/1614060 alleles, homozygotes = 0) and has highest observed frequency in the Ashkenazi Jewish population (AF= 0.000101351; MAF= 0.01014%, 3/29600 alleles, homozygotes = 0); grpmax FAF= 2.074e-05.
      Overall AF
      13 / 251,436
      0.0052%
      Highest · Ashkenazi Jewish
      0.04%
      Homozygotes
      0
      grpmax FAF
      0.0034%
      Allele frequency by ancestry — gnomAD v2.1
      observed in 3 of 8 groups
      AncestryAllele countFrequencyHomozygotes
      Ashkenazi Jewish 4 / 10,070 0.04% 0
      European (non-Finnish) 8 / 113,740 0.007% 0
      Admixed American 1 / 34,584 0.0029% 0
      African/African American 0 / 16,256
      East Asian 0 / 18,392
      European (Finnish) 0 / 21,642
      Remaining individuals 0 / 6,136
      South Asian 0 / 30,616
      This variant is present in gnomAD v2.1 (AF= 5.1703e-05; MAF= 0.00517%, 13/251436 alleles, homozygotes = 0) and has highest observed frequency in the Ashkenazi Jewish population (AF= 0.000397219; MAF= 0.03972%, 4/10070 alleles, homozygotes = 0); grpmax FAF= 3.419e-05.
      Not available in gnomAD-Canada v1.0.
      ClinVar screenshot
      ClinVar
      Error retrieving ClinVar entry.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.735. BayesDel score = 0.13148.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. MYD88, an adaptor protein, is frequently altered in hematologic malignancies including Waldenström's macroglobulinemia.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV57169334, n = 2493 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Literature · 10 PMIDs triaged · 8 high-priority
      10papers screened
      Papers triaged by theme: functional/splicing/segregation/case_observation. high_priority_papers include abstract snippets. Use these to support PS3/BS3/PS4/PP1/PP3/PP5.
      21179087 ↗ splicing rna
      Oncogenically active MYD88 mutations in human lymphoma.
      The activated B-cell-like (ABC) subtype of diffuse large B-cell lymphoma (DLBCL) remains the least curable form of this malignancy despite recent advances in therapy. Constitutive nuclear factor (NF)-κB and JAK kinase signalling promotes malignant cell survival in these lymphomas, but the genetic basis for this signalling is incompletely understood. Here we describe the dependence of ABC DLB
      BP7PP3PP5PS4PVS1
      23836557 ↗ functional
      A mutation in MYD88 (L265P) supports the survival of lymphoplasmacytic cells by activation of Bruton tyrosine kinase in Waldenström macroglobulinemia.
      Myeloid differentiation factor 88 (MYD88) L265P somatic mutation is highly prevalent in Waldenström macroglobulinemia (WM) and supports malignant growth through nuclear factor κB (NF-κB). The signaling cascade(s) by which MYD88 L265P promotes NF-κB activation in WM remain unclear. By lentiviral knockdown or use of a MYD88 inhibitor, decreased phosphorylation of the NF-&#x3ba
      BS3PP5PS3PS4
      35101336 ↗ functional
      Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC).
      Several professional societies have published guidelines for the clinical interpretation of somatic variants, which specifically address diagnostic, prognostic, and therapeutic implications. Although these guidelines for the clinical interpretation of variants include data types that may be used to determine the oncogenicity of a variant (eg, population frequency, functional, and in silico data or
      BS3PP5PS3PS4
      22918138 ↗ case observation
      Opportunities and challenges associated with clinical diagnostic genome sequencing: a report of the Association for Molecular Pathology.
      This report of the Whole Genome Analysis group of the Association for Molecular Pathology illuminates the opportunities and challenges associated with clinical diagnostic genome sequencing. With the reality of clinical application of next-generation sequencing, technical aspects of molecular testing can be accomplished at greater speed and with higher volume, while much information is obtained. Al
      PP5PS4
      22931316 ↗ case observation
      MYD88 L265P somatic mutation in Waldenström's macroglobulinemia.
      Waldenström's macroglobulinemia is an incurable, IgM-secreting lymphoplasmacytic lymphoma (LPL). The underlying mutation in this disorder has not been delineated. We performed whole-genome sequencing of bone marrow LPL cells in 30 patients with Waldenström's macroglobulinemia, with paired normal-tissue and tumor-tissue sequencing in 10 patients. Sanger sequencing was used to validate the
      PP5PS4
      23215570 ↗ hotspot domain
      MYD88 L265P somatic mutation in IgM MGUS.
      PM1PP5PS4
      23355535 ↗ case observation
      Prevalence and clinical significance of the MYD88 (L265P) somatic mutation in Waldenstrom's macroglobulinemia and related lymphoid neoplasms.
      A study has shown that MYD88 (L265P) is a recurring somatic mutation in Waldenström's macroglobulinemia (WM). We developed an allele-specific polymerase chain reaction (PCR) for this mutation, and analyzed bone marrow or peripheral blood samples from 58 patients with WM, 77 with IgM monoclonal gammopathy of undetermined significance (IgM-MGUS), 84 with splenic marginal zone lymphoma (SMZL), a
      PP5PS4
      34131312 ↗ case observation
      Chromosomal microarray analysis, including constitutional and neoplastic disease applications, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG).
      Chromosomal microarray technologies, including array comparative genomic hybridization and single-nucleotide polymorphism array, are widely applied in the diagnostic evaluation for both constitutional and neoplastic disorders. In a constitutional setting, this technology is accepted as the first-tier test for the evaluation of chromosomal imbalances associated with intellectual disability, autism,
      PP5PS4
      23619274 ↗ background review
      American College of Medical Genetics and Genomics technical standards and guidelines: microarray analysis for chromosome abnormalities in neoplastic disorders.
      PP5PS4
      28492532 ↗ background review
      Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
      PP5PS4
      Sources & reference links
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots