Is MAP2K2 p.Leu387= (c.1159C>T) pathogenic?

MAP2K2 p.Leu387= (c.1159C>T) is classified Likely benign in MAP2K2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-02-22). Very rare (popmax 0.00545%, afr); Associated with RASopathy.

What condition is associated with MAP2K2 p.Leu387= (c.1159C>T)?

MAP2K2 p.Leu387= (c.1159C>T) is associated with RASopathy (ClinVar).

How common is MAP2K2 p.Leu387= (c.1159C>T) in the general population?

MAP2K2 p.Leu387= (c.1159C>T) is very rare (popmax 0.00545%, afr) (gnomAD).

MAP2K2 p.Leu387=

c.1159C>T · rs1172594212 · VCV1635966

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00545%, afr)

Conditions

RASopathy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.3	GERP -3.9, phastCons 1
Overall
CADD	12.07	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00545% African / African-American · 4/73,408 alleles

Filtering AF 0.00177% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00106%

Overall 0.000321% 5/1,556,812 alleles · very rare exomes 2/1,404,592 · genomes 3/152,220 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00545%	18,352
Remaining individualsnot grpmax-eligible	0.00166%	60,296

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: MAP2K2
Protein: p.Leu387=
Coding: c.1159C>T
MANE Select: NM_030662
dbSNP: rs1172594212
Type: single nucleotide variant
Location: chr19:4090642 (GRCh38)
Gene constraint: LOEUF 0.858 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.54 · 3 PDB
Residue 387: an α-helix

Full MAP2K2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

RASopathy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MAP2K2 p.Leu387Val Uncertain significance ★ ⚠ same residue
MAP2K2 p.Glu207Lys Likely pathogenic ★★★ same condition
MAP2K2 p.Phe57Cys Pathogenic ★★★ same condition
MAP2K2 p.Pro128Gln Pathogenic ★★★ same condition
MAP2K2 p.Tyr134Cys Likely pathogenic ★★★ same condition
MAP2K2 p.Tyr134His Pathogenic ★★★ same condition
MAP2K2 p.Arg231His Uncertain significance ★★★ ⚠ same condition
MAP2K2 p.Arg231Leu Uncertain significance ★★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/map2k2-p-leu387 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown