PGM3 p.Ser137fs
c.408_409del · VCV4724272
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
immunodeficiency 23
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 4 of 13 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.4 | GERP 1.2, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- PGM3
- Protein
- p.Ser137fs
- Coding
- c.408_409del
- MANE Select
- NM_015599
- Type
- Deletion
- Location
- chr6:83187056 (GRCh38)
- Gene constraint
- LOEUF 0.962 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 95.54
Disease context
immunodeficiency 23 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor PGM3-CDG (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Childhood, Infancy, Neonatal
Similar variants
- PGM3 p.Ser137= Likely benign ★★ same residue
- PGM3 p.Ser137Pro Uncertain significance ★ ⚠ same residue
- PGM3 p.Leu452fs Pathogenic ★★ same condition
- PGM3 p.Lys54fs Pathogenic ★★ same condition
- PGM3 p.Met385fs Pathogenic/Likely pathogenic ★★ same condition
- PGM3 p.Ser133fs Pathogenic ★★ same condition
- PGM3 c.390-232_417del Likely pathogenic ★ same condition
- PGM3 c.-2-238del 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/pgm3-p-ser137fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown