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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
      v4.1
      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.
      v2.1
      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.
      🇨🇦 CA
      Not available in gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0026% · 42 / 1,614,060
      0 hom · FAF 0.0021%
      Ashkenazi Jewish
      3 / 29,600
      0.01%
      Admixed American
      2 / 60,016
      0.0033%
      European (non-Finnish)
      34 / 1,179,918
      0.0029%
      East Asian
      1 / 44,870
      0.0022%
      Remaining individuals
      1 / 62,508
      0.0016%
      South Asian
      1 / 91,084
      0.0011%
      + 4 not observed (European (Finnish), Amish, Middle Eastern, African/African American)
      gnomAD v2.1
      0.0052% · 13 / 251,436
      0 hom · FAF 0.0034%
      Ashkenazi Jewish
      4 / 10,070
      0.04%
      European (non-Finnish)
      8 / 113,740
      0.007%
      Admixed American
      1 / 34,584
      0.0029%
      + 5 not observed (African/African American, East Asian, European (Finnish), Remaining individuals, South Asian)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      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 · how each cited paper was used
      5papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 5 further PMIDs triaged but not cited — see Sources & References.
      Oncogenically active MYD88 mutations in human lymphoma.
      Searched
      c.818T>Cp.Leu273ProL265PL273P
      Found
      MYD88 L265P (Leu273Pro) was identified as a recurrent somatic mutation in activated B-cell-like diffuse large B-cell lymphoma (ABC DLBCL), constitutively activating NF-kappaB and JAK/STAT signaling. Knockdown of MYD88 selectively killed L265P-mutant ABC DLBCL cell lines but not wild-type cells.
      Variant
      ✓ Names this variant
      Applied to
      PS3 supports · met
      Why
      Demonstrated gain-of-function pathogenic mechanism; primary functional evidence for PS3_strong. Also assessed under BS3 where damaging effect contradicts benign interpretation.
      MYD88 L265P somatic mutation in Waldenström's macroglobulinemia.
      Searched
      c.818T>Cp.Leu273ProL265PL273P
      Found
      MYD88 L265P was detected in over 90% of Waldenstrom macroglobulinemia (WM) cases by whole-genome sequencing of lymphoplasmacytic cells from 30 patients. NF-kappaB activation was confirmed in primary WM cells harboring the mutation.
      Variant
      ✓ Names this variant
      Applied to
      PS3 supports · met PS4 supports · met
      Why
      Supported PS3_strong through confirmation of NF-kappaB activation in primary cells, and PS4_strong by establishing high prevalence in affected individuals.
      MYD88 L265P somatic mutation in IgM MGUS.
      Searched
      c.818T>Cp.Leu273ProL265PL273P
      Found
      MYD88 L265P was identified in IgM-MGUS and shown to localize to the TIR domain BB-loop, a critical functional motif for MYD88 signal transduction and a known mutational hotspot in hematologic malignancies.
      Variant
      ✓ Names this variant
      Applied to
      PM1 supports · met PS4 supports · met
      Why
      Supported PS4_strong by documenting L265P in IgM-MGUS precursor state, and PM1_moderate by confirming location in the TIR domain BB-loop mutational hotspot.
      Prevalence and clinical significance of the MYD88 (L265P) somatic mutation in Waldenstrom's macroglobulinemia and related lymphoid neoplasms.
      Searched
      c.818T>Cp.Leu273ProL265PL273P
      Found
      MYD88 L265P was detected in 96% of Waldenstrom macroglobulinemia cases and 54% of IgM monoclonal gammopathy of undetermined significance (IgM-MGUS) cases by allele-specific PCR, establishing L265P as a highly prevalent and early mutational event in WM pathogenesis.
      Variant
      ✓ Names this variant
      Applied to
      PS4 supports · met
      Why
      Strengthened PS4_strong by expanding the known prevalence of L265P in WM and demonstrating its presence in pre-malignant IgM-MGUS.
      A mutation in MYD88 (L265P) supports the survival of lymphoplasmacytic cells by activation of Bruton tyrosine kinase in Waldenström macroglobulinemia.
      Searched
      c.818T>Cp.Leu273ProL265PL273P
      Found
      MYD88 L265P activated BTK and NF-kappaB signaling in lymphoplasmacytic cells. Pharmacologic inhibition of BTK with ibrutinib selectively reduced survival of L265P-expressing cells, indicating dependence on the MYD88-BTK signaling axis.
      Variant
      ✓ Names this variant
      Applied to
      PS3 supports · met
      Why
      Provided independent functional confirmation of gain-of-function effect and therapeutic vulnerability; referenced in PS3_strong. Also assessed under BS3 where damaging effect contradicts benign interpretation.
      Sources & reference links
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 5 PMIDs not cited in assessment
      35101336 ↗ 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). CLINVAR
      22918138 ↗ Opportunities and challenges associated with clinical diagnostic genome sequencing: a report of the Association for Molecular Pathology. CLINVAR
      34131312 ↗ Chromosomal microarray analysis, including constitutional and neoplastic disease applications, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG). CLINVAR
      23619274 ↗ American College of Medical Genetics and Genomics technical standards and guidelines: microarray analysis for chromosome abnormalities in neoplastic disorders. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR