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MAP2K1
Final classification
VUS
MAP2K1 c.146G>A · p.Arg49His
MAP2K1

NM_002755.3:c.146G>A (p.Arg49His) in MAP2K1 is a missense variant located within the VCEP-designated critical functional domain spanning amino acids 43-61, satisfying PM1 at Moderate strength.

Gene
MAP2K1
Transcript
NM_002755.3
HGVS · transcript:coding
NM_002755.3:c.146G>A
Consequence
N/A
GRCh38
chr15:66435092 G>A
GRCh37
chr15:66727430 G>A
Basis ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MAP2K1 Version 2.3.0 v2.3.0 criteria-combination framework was evaluated deterministically with applied criteria: PS2 moderate, PM1 moderate, PP3 supporting; no rule matched the adjudicated criteria.
ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MAP2K1 Version 2.3.0 v2.3.0 criteria-combination framework was evaluated deterministically with applied criteria: PS2 moderate, PM1 moderate, PP3 supporting; no rule matched the adjudicated criteria.
Classification rationale
PS2PM1PP3 VUS
MAP2K1 c.146G>A

NM_002755.3:c.146G>A (p.Arg49His) in MAP2K1 is a missense variant located within the VCEP-designated critical functional domain spanning amino acids 43-61, satisfying PM1 at Moderate strength.1 A confirmed de novo occurrence of this variant was reported in a patient with cardio-facio-cutaneous syndrome, with both maternity and paternity confirmed, satisfying PS2 at Moderate strength (1 point under VCEP scoring). The REVEL in silico score is 0.707, meeting the VCEP PP3 threshold of ≥0.7 for missense variants at Supporting strength.2 This variant is present at extremely low frequency in gnomAD (AF ~0.0004%), far below both the BA1 (≥0.05%) and BS1 (≥0.025%) thresholds, and present in only 1 allele in v2.1 and 5 alleles in v4.1.3 No alternative pathogenic missense change at codon 49 was identified (PM5 not met), and the variant is not absent from gnomAD controls (PM2 not met per VCEP requirement for complete absence).4 PP2 (missense constraint z-score) remains unassessed pending gnomAD constraint data retrieval. If the MAP2K1 missense z-score exceeds 3.09, PP2_Supporting would also be met.5 ClinVar lists this variant as Uncertain significance (1 submitter, SCV003504233, Labcorp Genetics). No expert panel classification is available.6 Under the RASopathy VCEP v2.3.0 combination rules, the current met criteria (PM1_Moderate + PS2_Moderate + PP3_Supporting) do not satisfy any rule for Likely Pathogenic or Pathogenic classification. If PP2_Supporting is also met, Rule14 (2 Moderate + ≥2 Supporting) would be satisfied, yielding Likely Pathogenic.7

PS2 + PM1 + PP3 VUS
Gene diagram · NM_002755.3 · variants mapped to exon structure
MAP2K1 NM_002755.3
Fetching transcript structure from UCSC…
Applied criteria · 3 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
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      Population frequency
      Overall AF
      5 / 1,614,100
      0.00031%
      Highest · Admixed American
      0.0017%
      Homozygotes
      0
      grpmax FAF
      7.9e-05%
      Allele frequency by ancestry — gnomAD v4.1
      observed in 2 of 9 groups
      AncestryAllele countFrequencyHomozygotes
      Admixed American 1 / 60,010 0.0017% 0
      European (non-Finnish) 4 / 1,179,980 0.00034% 0
      European (Finnish) 0 / 64,034
      Amish 0 / 912
      East Asian 0 / 44,878
      Middle Eastern 0 / 6,060
      South Asian 0 / 91,074
      Ashkenazi Jewish 0 / 29,606
      African/African American 0 / 75,042
      This variant is present in gnomAD v4.1 (AF= 3.0977e-06; MAF= 0.00031%, 5/1614100 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 1.66639e-05; MAF= 0.00167%, 1/60010 alleles, homozygotes = 0); grpmax FAF= 7.9e-07.
      Overall AF
      1 / 251,360
      0.0004%
      Highest · Admixed American
      0.0029%
      Homozygotes
      0
      Allele frequency by ancestry — gnomAD v2.1
      observed in 1 of 8 groups
      AncestryAllele countFrequencyHomozygotes
      Admixed American 1 / 34,588 0.0029% 0
      African/African American 0 / 16,256
      Ashkenazi Jewish 0 / 10,076
      East Asian 0 / 18,394
      European (Finnish) 0 / 21,648
      European (non-Finnish) 0 / 113,648
      Remaining individuals 0 / 6,136
      South Asian 0 / 30,614
      This variant is present in gnomAD v2.1 (AF= 3.97836e-06; MAF= 0.00040%, 1/251360 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 2.89118e-05; MAF= 0.00289%, 1/34588 alleles, homozygotes = 0).
      This variant is absent from gnomAD-Canada.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 2185892)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.707. BayesDel score = 0.13946.
      Functional / OncoKB screenshot
      Functional Likely Neutral
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Neutral; curated oncogenicity label: Likely Neutral.
      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; COSV61070158, n = 4 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Literature · 2 PMIDs triaged · 1 high-priority
      2papers 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.
      32641410 ↗ functional
      Leveraging Systematic Functional Analysis to Benchmark an In Silico Framework Distinguishes Driver from Passenger MEK Mutants in Cancer.
      Despite significant advances in cancer precision medicine, a significant hurdle to its broader adoption remains the multitude of variants of unknown significance identified by clinical tumor sequencing and the lack of biologically validated methods to distinguish between functional and benign variants. Here we used functional data on MAP2K1 and MAP2K2 mutations generated in real-time within a co-c
      BS3PM1PS3
      28492532 ↗ background review
      Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
      PP5PS4
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots