NM_003010.3:c.400C>T

MAP2K4 · NP_003001.1:p.(Arg134Trp) · NM_003010.3

GRCh37: chr17:11998898 C>T · GRCh38: chr17:12095581 C>T

Gene: MAP2K4 Transcript: NM_003010.3

Final call

VUS

PM1 moderate PM2 moderate

Variant details

Gene

MAP2K4

Transcript

NM_003010.3

Protein

NP_003001.1:p.(Arg134Trp)

gnomAD AF

6.198175505058332e-07 (v4.1)

ClinVar

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

MAP2K4 c.400C>T (p.Arg134Trp) is a missense variant located at a well-established mutational hotspot (PM1_moderate) in the β3-αC loop of the kinase domain. It is the most frequent MKK4 mutation catalogued in COSMIC and lies within a statistically significant hotspot domain as defined by cancerhotspots.org.

This variant is absent from gnomAD v2.1 and gnomAD-Canada, and is observed at an extremely low frequency in gnomAD v4.1 (1/1,613,378 alleles; AF=6.2×10⁻⁷), meeting the PM2 criterion for very low population frequency (PM2_moderate).

Computational in silico predictors are indeterminate: REVEL (0.475) and BayesDel (0.247) fall below established pathogenic thresholds, and SpliceAI predicts no splice alteration. PP3 is not met.

Molecular dynamics simulations (PMID:33101607) demonstrate that p.Arg134Trp introduces a TRP134-TRP134 π-π interaction that distorts the N-lobe dimer interface of autoinhibited MKK4, but this computational evidence does not independently meet PS3 criteria for well-established functional evidence.

The variant is absent from ClinVar and no clinical laboratory or expert panel classification is available. No de novo, segregation, case-control, or experimental functional data were identified for this variant.

Two pathogenic criteria of moderate strength are met (PM1 and PM2). Under generic ACMG/AMP 2015 combination rules (PMID:25741868), two moderate criteria are insufficient to reach a Likely Pathogenic classification, which requires at least three moderate criteria or two moderate plus two supporting criteria. The variant is classified as a Variant of Uncertain Significance (VUS).

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	PVS1 applies only to null variants (nonsense, frameshift, canonical ±1/2 splice); NM_003010.3:c.400C>T is a missense variant (p.Arg134Trp) and does not fall into any default generic PVS1 null-variant bucket per PMC6185798.	pvs1_generic_framework
PS1	Not met	No prior observation of a different nucleotide change at the same amino acid (p.Arg134) with a pathogenic classification has been identified in ClinVar or published literature.	clinvar
PS2	Not met	No de novo observation with confirmed maternity and paternity has been identified for NM_003010.3:c.400C>T.
PS3	Not met	No well-established in vitro or in vivo functional assay data exist for p.Arg134Trp. PMID:33101607 provides molecular dynamics simulations showing altered dimer interface interactions but this is computational modeling, not a validated functional assay. OncoKB annotation of 'Likely Loss-of-function' is a curated inference, not primary functional evidence meeting PS3 threshold.	PMID:33101607 oncokb
PS4	Not met	No case-control or aggregate cohort data comparing variant prevalence in affected individuals versus controls have been identified for this variant.
PS5	Not met	No reputable source has independently reported this variant as pathogenic; absent from ClinVar and no diagnostic laboratory classification identified.	clinvar
PM1	Met	p.Arg134Trp (R134W) lies at a well-established mutational hotspot in MAP2K4. It is identified as one of two COSMIC hotspot mutations (R134W and S184L) and is located in a statistically significant hotspot domain (β3-αC loop), as confirmed by cancerhotspots.org and PMID:33101607.	PMID:33101607
PM2	Met	NM_003010.3:c.400C>T is absent from gnomAD v2.1 and gnomAD-Canada, and is present in gnomAD v4.1 at an extremely low allele frequency of 6.2×10⁻⁷ (1/1,613,378 alleles; highest subpopulation NFE AF=8.5×10⁻⁷). This frequency is well below the 0.1% threshold for PM2.	gnomad_v2 gnomad_v4 gnomad_canada
PM3	N/A	PM3 applies to variants observed in trans with a pathogenic variant for recessive disorders; no trans-configuration data available and MAP2K4-associated disorders are not established as recessive.
PM4	N/A	PM4 applies to protein-length altering variants (in-frame indels, stop-loss, initiation codon); NM_003010.3:c.400C>T is a missense substitution.
PM5	N/A	No same-residue comparator variant with a pathogenic classification has been identified at p.Arg134 to support PM5 application; automated PM5 candidate harvesting returned no eligible candidates.	pm5_candidates
PM6	Not met	No de novo observation (assumed de novo without confirmation of maternity/paternity) has been identified for NM_003010.3:c.400C>T.
PP1	Not met	No co-segregation data in affected family members have been identified for this variant.
PP2	Not assessed	Insufficient data to determine whether MAP2K4 has a low rate of benign missense variation and whether missense variants are a common mechanism of disease. HCI prior data are unavailable for MAP2K4.
PP3	Not met	In silico predictors do not support a deleterious effect: REVEL score is 0.475 (below 0.5 pathogenic threshold), BayesDel score is 0.247 (below ~0.27 pathogenic threshold), and SpliceAI max delta score is 0.00 indicating no predicted splice impact.	revel bayesdel spliceai
PP4	Not met	No patient phenotype or family history data are available to assess whether the clinical presentation is highly specific for a MAP2K4-related disorder.
PP5	Not met	No reputable source (diagnostic laboratory, expert panel) has reported this variant as pathogenic. The variant is absent from ClinVar.	clinvar
BA1	Not met	The variant has a maximum population allele frequency of 8.5×10⁻⁷ in gnomAD v4.1 (NFE), far below the BA1 threshold of >1%.	gnomad_v4
BS1	Not met	The variant has a total allele frequency of 6.2×10⁻⁷ in gnomAD v4.1, far below the BS1 threshold of >0.3%.	gnomad_v4
BS2	Not met	No observation of this variant in healthy adult individuals in the context of a fully penetrant disorder expected to manifest at an early age has been identified.
BS3	Not met	No well-established in vitro or in vivo functional studies demonstrating no damaging effect have been identified. PMID:33101607 is a computational MD simulation study and does not constitute an experimental functional assay.	PMID:33101607
BS4	Not met	No segregation data in affected families are available to demonstrate lack of co-segregation with disease.
BP1	Not met	BP1 applies when missense variants occur in a gene where primarily truncating variants cause disease. MAP2K4 has well-characterized pathogenic missense mutations at known hotspots (including p.Arg134 and p.Ser184), indicating that missense variants are a recognized disease mechanism, not only truncating variants.	PMID:33101607
BP2	N/A	BP2 requires observation in trans with a pathogenic variant in a fully penetrant dominant disorder, which requires specific genotypic and phase data not available for this variant.
BP3	N/A	BP3 applies to in-frame indels in repetitive regions; NM_003010.3:c.400C>T is a missense substitution.
BP4	Not met	Multiple lines of computational evidence do not confidently suggest no impact. REVEL score is 0.475 (borderline, just below 0.5 pathogenic threshold), BayesDel is 0.247 (below 0.27 pathogenic threshold but not clearly benign), and SpliceAI delta is 0.00. The aggregate in silico evidence is indeterminate rather than supportive of a benign interpretation.	revel bayesdel spliceai
BP5	Not met	No observation of this variant in a case with an alternate molecular basis for disease has been identified.
BP6	Not met	No reputable source has reported this variant as benign. The variant is absent from ClinVar.	clinvar
BP7	N/A	BP7 applies to synonymous variants with no predicted splice impact; NM_003010.3:c.400C>T is a missense substitution (p.Arg134Trp).

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