Is PGM1 p.Phe29fs (c.87_94del) pathogenic?

PGM1 p.Phe29fs (c.8794del) is classified Pathogenic in PGM1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-10-15). Very rare (popmax 0.000932%, nfe); Associated with PGM1-congenital disorder of glycosylation.

What condition is associated with PGM1 p.Phe29fs (c.87_94del)?

PGM1 p.Phe29fs (c.87_94del) is associated with PGM1-congenital disorder of glycosylation (ClinVar).

How common is PGM1 p.Phe29fs (c.87_94del) in the general population?

PGM1 p.Phe29fs (c.87_94del) is very rare (popmax 0.000932%, nfe) (gnomAD).

How is PGM1-CDG inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

PGM1 p.Phe29fs

c.87_94del · rs752562811 · VCV2581183

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.000932%, nfe)

Conditions

PGM1-congenital disorder of glycosylation

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 1 of 11
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.6	GERP 2.1, phastCons 1

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000932% European (non-Finnish) · 11/1,179,918 alleles

Filtering AF 0.0005% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000366%

Overall 0.000682% 11/1,613,774 alleles · very rare exomes 11/1,461,482 · genomes 0/152,292 · joint denominator

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: PGM1
Protein: p.Phe29fs
Coding: c.87_94del
MANE Select: NM_002633
dbSNP: rs752562811
Type: Deletion
Location: chr1:63593575 (GRCh38)
Gene constraint: LOEUF 1.189 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 97.27 · 16 PDB
Residue 29: an α-helix

Full PGM1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

PGM1-congenital disorder of glycosylation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For PGM1-CDG (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

PGM1 p.Asn364fs Pathogenic ★★ same condition
PGM1 p.Ala142fs Pathogenic ★ same condition
PGM1 p.Arg221fs Pathogenic ★ same condition
PGM1 p.Ile500fs Pathogenic ★ same condition
PGM1 p.Leu492fs Pathogenic ★ same condition
PGM1 p.Pro231_Tyr232insTer Pathogenic ★ same condition
PGM1 c.1145-6del Benign ★ same condition
PGM1 c.1465-16_1465-15del Likely benign ★ 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/pgm1-p-phe29fs (accessed [today's date]).

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