PFKM p.Arg201=
c.601A>C · rs2498343865 · VCV2795081
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
glycogen storage disease VII
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.5 | GERP -0.83, phastCons 1 |
| Overall | ||
| CADD | 13.05 | 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
- PFKM
- Protein
- p.Arg201=
- Coding
- c.601A>C
- MANE Select
- NM_000289
- dbSNP
- rs2498343865
- Type
- single nucleotide variant
- Location
- chr12:48134239 (GRCh38)
- Gene constraint
- LOEUF 0.774 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.66 · 1 PDB
- Residue 201
- a binding site; the 'n-terminal catalytic pfk domain 1' region
Disease context
glycogen storage disease VII — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Glycogen storage disease due to muscle phosphofructokinase deficiency (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adolescent, Adult, Childhood, Infancy
Similar variants
- PFKM c.1062+1G>A Likely pathogenic ★★ same condition
- PFKM c.1128-2A>G Likely pathogenic ★★ same condition
- PFKM c.1191+1G>A Likely pathogenic ★★ same condition
- PFKM c.1412+1G>T Likely pathogenic ★★ same condition
- PFKM c.1412+2T>C Likely pathogenic ★★ same condition
- PFKM c.1413-2A>G Pathogenic/Likely pathogenic ★★ same condition
- PFKM c.1413-64A>G Pathogenic/Likely pathogenic ★★ same condition
- PFKM c.1500+1G>A 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/pfkm-p-arg201 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown