Is MAP2K1 p.Asp16fs (c.45del) pathogenic?

MAP2K1 p.Asp16fs (c.45del) is classified Uncertain significance in MAP2K1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2018-09-16). No allele count reported in gnomAD v4.1 (AN 1,565,938).

How common is MAP2K1 p.Asp16fs (c.45del) in the general population?

MAP2K1 p.Asp16fs (c.45del) is no allele count reported in gnomAD v4.1 (AN 1,565,938) (gnomAD).

MAP2K1 p.Asp16fs

c.45del · rs1566991692 · VCV591639

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,565,938)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 1 of 11
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 5.8	GERP 0.34, phastCons 1

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,565,938). 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: MAP2K1
Protein: p.Asp16fs
Coding: c.45del
MANE Select: NM_002755
dbSNP: rs1566991692
Type: Deletion
Location: chr15:66387388 (GRCh38)
Gene constraint: LOEUF 0.515 · pLI 0.97 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 84.05 · 99 PDB
Residue 16: the 'disordered' region

Full MAP2K1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

MAP2K1 p.Asp16Glu Uncertain significance ★★ ⚠ same residue
MAP2K1 p.Gln58_Glu62del Pathogenic/Likely pathogenic ★★ same type
MAP2K1 p.Ile103_Lys104del Pathogenic/Likely pathogenic ★★ same type
MAP2K1 p.Lys59del Likely pathogenic ★★ same type
MAP2K1 p.Gly281del Uncertain significance ★★ same type
MAP2K1 c.292-13del Benign ★★ same type
MAP2K1 c.896-5del Likely benign ★★ same type
MAP2K1 p.Gln56_Val60del Likely pathogenic ★ 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/map2k1-p-asp16fs (accessed [today's date]).

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