Is PHKB p.Ile876= (c.2628C>T) pathogenic?

PHKB p.Ile876= (c.2628C>T) is classified Likely benign in PHKB (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-28). Ultra-rare (popmax 0.012%, afr); Associated with glycogen storage disease IXb.

What condition is associated with PHKB p.Ile876= (c.2628C>T)?

PHKB p.Ile876= (c.2628C>T) is associated with glycogen storage disease IXb (ClinVar).

How common is PHKB p.Ile876= (c.2628C>T) in the general population?

PHKB p.Ile876= (c.2628C>T) is ultra-rare (popmax 0.012%, afr) (gnomAD).

PHKB p.Ile876=

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.2628C>T · rs17812908 · VCV2194052

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.012%, afr)

Conditions

glycogen storage disease IXb

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.32	GERP -5.5, phastCons 0.28
Overall
CADD	5.748	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.012% African / African-American · 9/74,880 alleles

Filtering AF 0.00624% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00468%

Overall 0.00136% 22/1,613,492 alleles · ultra-rare exomes 19/1,461,368 · genomes 3/152,124 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.012%	8,320
East Asian	0.00445%	22,448
South Asian	0.0011%	91,062
European (non-Finnish)	0.000848%	117,957

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: PHKB
Protein: p.Ile876=
Coding: c.2628C>T
MANE Select: NM_000293
dbSNP: rs17812908
Type: single nucleotide variant
Location: chr16:47669415 (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 876: 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.Ile876Val Uncertain significance ★ ⚠ same residue
PHKB p.Ile876Met Uncertain significance ★ ⚠ same residue
PHKB c.1127-2A>G Pathogenic/Likely pathogenic ★★ same condition
PHKB c.1364-2A>G Pathogenic ★★ same condition
PHKB c.1972-2A>G Pathogenic/Likely pathogenic ★★ same condition
PHKB c.2427+965A>C Pathogenic/Likely pathogenic ★★ same condition
PHKB c.2896-1G>T Pathogenic ★★ same condition
PHKB c.306-2A>G 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/phkb-p-ile876 (accessed [today's date]).

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