Is PHKA1 p.Pro951fs (c.2847_2848del) pathogenic?

PHKA1 p.Pro951fs (c.28472848del) is classified Pathogenic in PHKA1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-17). Associated with glycogen storage disease IXd.

What condition is associated with PHKA1 p.Pro951fs (c.2847_2848del)?

PHKA1 p.Pro951fs (c.2847_2848del) is associated with glycogen storage disease IXd (ClinVar).

PHKA1 p.Pro951fs

Q: How is Glycogen storage disease due to muscle phosphorylase kinase deficiency inherited?

Typically Autosomal recessive, X-linked recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.2847_2848del · VCV3721392

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

glycogen storage disease IXd

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 26 of 32
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.6	phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Variant & gene context

Gene: PHKA1
Protein: p.Pro951fs
Coding: c.2847_2848del
MANE Select: NM_002637
Type: Deletion
Location: chrX:72603188 (GRCh38)
Structure: AlphaFold pLDDT 81.84 · 10 PDB
Residue 951: an α-helix

Full PHKA1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

glycogen storage disease IXd — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Glycogen storage disease due to muscle phosphorylase kinase deficiency (Orphanet):

Inheritance: Autosomal recessive, X-linked recessive
Onset: Adolescent, Adult

Similar variants

PHKA1 p.Glu449fs Likely pathogenic ★★ same condition
PHKA1 p.Cys238fs Pathogenic ★ same condition
PHKA1 p.Val227fs Likely pathogenic ★ same condition
PHKA1 c.1459+6_1459+8del Conflicting classifications of pathogenicity ★ same condition
PHKA1 p.Ser701_Leu702del Uncertain significance ★ same condition
PHKA1 c.3244-12del Benign ★ same condition
PHKA1 p.Pro951= Likely benign ★ same residue
PHKA1 p.Ala232fs 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/phka1-p-pro951fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown