Is PHKB p.Asp318Ter (c.951dup) pathogenic?

PHKB p.Asp318Ter (c.951dup) is classified Likely pathogenic in PHKB (ClinVar, Single submitter, 1 submitter). Absent from gnomAD; Associated with glycogen storage disease IXb.

What condition is associated with PHKB p.Asp318Ter (c.951dup)?

PHKB p.Asp318Ter (c.951dup) is associated with glycogen storage disease IXb (ClinVar).

How common is PHKB p.Asp318Ter (c.951dup) in the general population?

PHKB p.Asp318Ter (c.951dup) is absent from gnomAD (gnomAD).

PHKB p.Asp318Ter

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

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

c.951dup · rs2506377578 · VCV2664187

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

glycogen storage disease IXb

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 10 of 31
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6	GERP 2, phastCons 1

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

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PHKB
Protein: p.Asp318Ter
Coding: c.951dup
MANE Select: NM_000293
dbSNP: rs2506377578
Type: Duplication
Location: chr16:47588983 (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 318: an α-helix

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

Disease context

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

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

Inheritance: Autosomal recessive
Onset: Childhood

Similar variants

PHKB p.Asn422fs Pathogenic ★★ same condition
PHKB c.3144+33_3144+34dup Benign ★★ same condition
PHKB c.594+1dup Likely pathogenic ★ same condition
PHKB p.Gln389fs Pathogenic ★ same condition
PHKB p.Gln603fs Pathogenic ★ same condition
PHKB p.Gln809fs Pathogenic ★ same condition
PHKB p.Glu115fs Pathogenic ★ same condition
PHKB p.Gly940fs 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-asp318ter (accessed [today's date]).

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