PHKB p.Arg482fs
c.1446del · VCV3580742
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
glycogen storage disease IXb
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 14 of 31 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 1 | GERP 0.92, phastCons 0.99 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- PHKB
- Protein
- p.Arg482fs
- Coding
- c.1446del
- MANE Select
- NM_000293
- Type
- Deletion
- Location
- chr16:47610907 (GRCh38)
- Gene constraint
- LOEUF 0.792 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 87.06 · 6 PDB
- Residue 482
- a turn
Disease context
glycogen storage disease IXb — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Glycogen storage disease due to liver and muscle phosphorylase kinase deficiency (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Childhood
Similar variants
- PHKB p.Arg482= Benign/Likely benign ★★ same residue
- PHKB p.Glu820fs Pathogenic/Likely pathogenic ★★ same condition
- PHKB p.Val175fs Pathogenic/Likely pathogenic ★★ same condition
- PHKB c.2427+964del Likely benign ★★ same condition
- PHKB c.3144+34del Benign/Likely benign ★★ same condition
- PHKB c.1363+1del Likely pathogenic ★ same condition
- PHKB c.167-6_170del Likely pathogenic ★ same condition
- PHKB c.2329_2336+5del 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/phkb-p-arg482fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown