Is PGM3 p.Ser491= (c.1473T>C) pathogenic?

PGM3 p.Ser491= (c.1473T>C) is classified Likely benign in PGM3 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-25). Absent from gnomAD v4.1; Associated with immunodeficiency 23.

What condition is associated with PGM3 p.Ser491= (c.1473T>C)?

PGM3 p.Ser491= (c.1473T>C) is associated with immunodeficiency 23 (ClinVar).

How common is PGM3 p.Ser491= (c.1473T>C) in the general population?

PGM3 p.Ser491= (c.1473T>C) is absent from gnomAD v4.1 (gnomAD).

How is PGM3-CDG inherited?

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

PGM3 p.Ser491=

c.1473T>C · rs1786852929 · VCV1138090

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

immunodeficiency 23

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -0.15	GERP -5.5, phastCons 0.089
Overall
CADD	1.982	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: PGM3
Protein: p.Ser491=
Coding: c.1473T>C
MANE Select: NM_015599
dbSNP: rs1786852929
Type: single nucleotide variant
Location: chr6:83170371 (GRCh38)

Full PGM3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

immunodeficiency 23 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For PGM3-CDG (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood, Infancy, Neonatal

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/pgm3-p-ser491 (accessed [today's date]).

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