PHKG2 p.Phe104=
c.312C>T · VCV3644357
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 IXc
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 2.5, phastCons 1 |
| Overall | ||
| CADD | 14.13 | 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
- PHKG2
- Protein
- p.Phe104=
- Coding
- c.312C>T
- MANE Select
- NM_000294
- Type
- single nucleotide variant
- Location
- chr16:30751589 (GRCh38)
- Gene constraint
- LOEUF 0.876 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 83.77 · 1 PDB
- Residue 104
- the protein kinase domain; a β-strand
Disease context
glycogen storage disease IXc — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Glycogen storage disease due to liver phosphorylase kinase deficiency (Orphanet):
- Inheritance
- Autosomal recessive, X-linked recessive
- Onset
- Childhood
- Prevalence
- 1-9 / 100 000 (Europe)
Similar variants
- PHKG2 c.96-11G>A Pathogenic/Likely pathogenic ★★ same condition
- PHKG2 p.Arg152Ter Pathogenic/Likely pathogenic ★★ same condition
- PHKG2 p.Arg185Ter Pathogenic ★★ same condition
- PHKG2 p.Arg279Cys Pathogenic/Likely pathogenic ★★ same condition
- PHKG2 p.Arg309Trp Likely pathogenic ★★ ⚠ same condition
- PHKG2 p.Arg44Ter Pathogenic ★★ same condition
- PHKG2 p.Arg76Ter Pathogenic/Likely pathogenic ★★ same condition
- PHKG2 p.Asp215Asn 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/phkg2-p-phe104 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown