Is MAP2K2 p.Asp69fs (c.206del) pathogenic?

MAP2K2 p.Asp69fs (c.206del) is classified Uncertain significance in MAP2K2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-08). No gnomAD frequency available for this variant.

How common is MAP2K2 p.Asp69fs (c.206del) in the general population?

MAP2K2 p.Asp69fs (c.206del) is no gnomAD frequency available for this variant (gnomAD).

MAP2K2 p.Asp69fs

c.206del · rs2145080289 · VCV1313319

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 2 of 11
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -4	GERP -3.9

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: MAP2K2
Protein: p.Asp69fs
Coding: c.206del
MANE Select: NM_030662
dbSNP: rs2145080289
Type: Deletion
Location: chr19:4117516 (GRCh38)
Gene constraint: LOEUF 0.858 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.54 · 3 PDB
Residue 69: an α-helix

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

Similar variants

MAP2K2 p.Asp69His Uncertain significance ★★ ⚠ same residue
MAP2K2 p.Asp69= Likely benign ★★ same residue
MAP2K2 p.Asp69Glu Uncertain significance ★ ⚠ same residue
MAP2K2 p.Leu54fs Uncertain significance ★★ same type
MAP2K2 c.303+15del Benign/Likely benign ★★ same type
MAP2K2 p.Asp71del Pathogenic ★ same type
MAP2K2 c.1046+5_1046+8del Uncertain significance ★ same type
MAP2K2 c.1046+5del Uncertain significance ★ same type

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-asp69fs (accessed [today's date]).

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