Is PHKA2 p.Ser907fs (c.2718del) pathogenic?

PHKA2 p.Ser907fs (c.2718del) is classified Likely pathogenic in PHKA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-25). Associated with glycogen storage disease IXa1.

What condition is associated with PHKA2 p.Ser907fs (c.2718del)?

PHKA2 p.Ser907fs (c.2718del) is associated with glycogen storage disease IXa1 (ClinVar).

PHKA2 p.Ser907fs

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

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

c.2718del · VCV4820149

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

glycogen storage disease IXa1

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 25 of 33
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.6	GERP -2.8, phastCons 1

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

Variant & gene context

Gene: PHKA2
Protein: p.Ser907fs
Coding: c.2718del
MANE Select: NM_000292
Type: Deletion
Location: chrX:18906583 (GRCh38)
Structure: AlphaFold pLDDT 81.36

Full PHKA2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

glycogen storage disease IXa1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For 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

PHKA2 p.Arg1072del Pathogenic/Likely pathogenic ★★ same condition
PHKA2 c.1794-8_1812del Pathogenic ★ same condition
PHKA2 c.285+2_285+5del Likely pathogenic ★ same condition
PHKA2 c.3329_3336+6del Pathogenic ★ same condition
PHKA2 c.455-5_463del Likely pathogenic ★ same condition
PHKA2 p.His501fs Pathogenic ★ same condition
PHKA2 p.Leu32fs Pathogenic ★ same condition
PHKA2 p.Leu822fs 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/phka2-p-ser907fs (accessed [today's date]).

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