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MAP2K1
Final classification
VUS
MAP2K1 c.158T>C · p.Phe53Ser
MAP2K1

The MAP2K1 c.158T>C (p.Phe53Ser) variant has been observed in somatic cancers in COSMIC and has been reported in ClinVar, including an expert panel submission classifying it as likely pathogenic.

Gene
MAP2K1
Transcript
NM_002755.4
HGVS · transcript:coding
NM_002755.4:c.158T>C
Consequence
N/A
GRCh38
chr15:66435104 T>C
GRCh37
chr15:66727442 T>C
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: PS3 supporting, PM1 moderate, PM2 supporting, PP3 supporting, PP5 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: PS3 supporting, PM1 moderate, PM2 supporting, PP3 supporting, PP5 supporting; no rule matched the adjudicated criteria.
Classification rationale
PS3PM1PM2PP3PP5 VUS
MAP2K1 c.158T>C

The MAP2K1 c.158T>C (p.Phe53Ser) variant has been observed in somatic cancers in COSMIC and has been reported in ClinVar, including an expert panel submission classifying it as likely pathogenic.1 This variant is absent from gnomAD v2.1 and gnomAD v4.1, supporting rarity in population reference datasets.2 Published functional studies of cardio-facio-cutaneous syndrome-associated MAP2K1 variants including F53S showed abnormal MAPK-pathway signaling, and the RASopathy VCEP recognizes MEK and ERK activation assays as approved functional assay types, supporting a damaging gain-of-function effect.3 Computational findings support a deleterious missense effect, with REVEL 0.938 above the VCEP PP3 threshold of 0.7, BayesDel 0.464442 in a damaging direction, and no predicted splice alteration by SpliceAI with a maximum delta score of 0.00.4

PS3 + PM1 + PM2 + PP3 + PP5 VUS
3 vcep_svi_rasopathy_vcep_v2_approved_functional_studiesPMID:17981815 ↗PMID:18413255 ↗
4 revelbayesdelspliceai ↗cspec ↗
Gene diagram · NM_002755.4 · variants mapped to exon structure
MAP2K1 NM_002755.4
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
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      Absent from gnomAD v4.1.
      v2.1
      Absent from gnomAD v2.1.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD v2.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Pathogenic (2 clinical laboratories) and as Likely Pathogenic by ClinGen RASopathy Variant Curation Expert Panel (expert panel).
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.938. BayesDel score = 0.464442.
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Gain-of-function; curated oncogenicity label: Likely Oncogenic.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV105128267, n = 2 times).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Literature · how each cited paper was used
      2papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why.
      PMID PMID:17981815
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PS3 supports · met
      PMID PMID:18413255
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PS3 supports · met
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots