PYGM p.Pro230fs
c.679_686dup · VCV3600069
Pathogenic/Likely pathogenic
Multiple submitters
Classification
Pathogenic/Likely pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
glycogen storage disease V
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 6 of 20 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -10 | GERP -3.9 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- PYGM
- Protein
- p.Pro230fs
- Coding
- c.679_686dup
- MANE Select
- NM_005609
- Type
- Duplication
- Location
- chr11:64755532 (GRCh38)
- Gene constraint
- LOEUF 0.962 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.41 · 1 PDB
- Residue 230
- a UniProt-annotated variant site (in gsd5); a β-strand
Disease context
glycogen storage disease V — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Glycogen storage disease due to muscle glycogen phosphorylase deficiency (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adolescent, Adult, Childhood
Similar variants
- PYGM p.Pro230= Likely benign ★ same residue
- PYGM p.Pro230Ser Uncertain significance ⚠ same residue
- PYGM p.Ala452fs Pathogenic ★★ same condition
- PYGM p.Arg490fs Pathogenic/Likely pathogenic ★★ same condition
- PYGM p.Asn168Ter Pathogenic/Likely pathogenic ★★ same condition
- PYGM p.Asp284fs Likely pathogenic ★★ same condition
- PYGM p.Leu137fs Likely pathogenic ★★ same condition
- PYGM p.Lys10fs 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/pygm-p-pro230fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown