Is PMM2 p.Lys115del (c.341AGA[1]) pathogenic?

PMM2 p.Lys115del (c.341AGA[1]) is classified Conflicting classifications of pathogenicity in PMM2 (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2026-06-02). No gnomAD frequency available for this variant; Associated with Inborn genetic diseases.

What condition is associated with PMM2 p.Lys115del (c.341AGA[1])?

PMM2 p.Lys115del (c.341AGA[1]) is associated with Inborn genetic diseases, PMM2-congenital disorder of glycosylation (ClinVar).

How common is PMM2 p.Lys115del (c.341AGA[1]) in the general population?

PMM2 p.Lys115del (c.341AGA[1]) is no gnomAD frequency available for this variant (gnomAD).

PMM2 p.Lys115del

c.341AGA[1] · rs1555449316 · VCV555501

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.9	GERP 1.9, phastCons 1

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: PMM2
Protein: p.Lys115del
Coding: c.341AGA[1]
MANE Select: NM_000303
dbSNP: rs1555449316
Type: Microsatellite
Location: chr16:8806399 (GRCh38)
Gene constraint: LOEUF 1.937 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 96.66 · 7 PDB

Full PMM2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: PMM2-congenital disorder of glycosylation

Similar variants

PMM2 p.Lys115= Likely benign ★ same residue
PMM2 c.451_454del Pathogenic/Likely pathogenic ★★ same condition
PMM2 p.Leu82fs Pathogenic ★★ same condition
PMM2 p.Phe68fs Pathogenic/Likely pathogenic ★★ same condition
PMM2 c.66+10_66+12del Likely benign ★ same condition
PMM2 c.178+1G>A Likely pathogenic ★★ same condition
PMM2 c.178+2T>G Likely pathogenic ★★ same condition
PMM2 c.179-1G>C Pathogenic/Likely pathogenic ★★ 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/pmm2-p-lys115del (accessed [today's date]).

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