Is MAP2K2 p.Leu275= (c.825G>A) pathogenic?

MAP2K2 p.Leu275= (c.825G>A) is classified Benign in MAP2K2 (ClinVar, Expert panel, 7 submitters; last evaluated 2017-05-09). Rare (popmax 0.134%, eas); Associated with RASopathy.

What condition is associated with MAP2K2 p.Leu275= (c.825G>A)?

MAP2K2 p.Leu275= (c.825G>A) is associated with RASopathy (ClinVar).

How common is MAP2K2 p.Leu275= (c.825G>A) in the general population?

MAP2K2 p.Leu275= (c.825G>A) is rare (popmax 0.134%, eas) (gnomAD).

MAP2K2 p.Leu275=

c.825G>A · rs587781027 · VCV138161

Benign Expert panel

Classification

Benign

ClinVar

Review

Expert panel ★★★☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

rare (popmax 0.134%, eas)

Conditions

RASopathy

ClinGen expert panel — RASopathy VCEP

Benign for RASopathy. Applied ACMG criteria (verbatim):

BA1

Curation rationale (ClinGen, verbatim)

The filtering allele frequency of the c.825G>A (p.Leu275=) variant in the MAP2K2 gene is 0.142% (14/5968) of East Asian chromosomes by the Exome Aggregation Consortium, which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen RASopathy Expert Panel (BA1; PMID:29493581)

ClinGen Evidence Repository → · reported verbatim, not re-tallied by Sugi Variant.

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 -0.11	GERP -0.58, phastCons 0.58
Overall
CADD	7.064	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.134% East Asian · 60/44,624 alleles

Filtering AF 0.107% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0973%

Overall 0.00386% 62/1,607,506 alleles · rare exomes 53/1,455,258 · genomes 9/152,248 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.134%	744
Remaining individualsnot grpmax-eligible	0.00321%	31,120

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.Leu275=
Coding: c.825G>A
MANE Select: NM_030662
dbSNP: rs587781027
Type: single nucleotide variant
Location: chr19:4099295 (GRCh38)
Gene constraint: LOEUF 0.858 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.54 · 3 PDB
Residue 275: the protein kinase domain; 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.Leu275Val 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-leu275 (accessed [today's date]).

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