Is PHKA2 p.Pro28= (c.84C>T) pathogenic?

PHKA2 p.Pro28= (c.84C>T) is classified Likely benign in PHKA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-03). Very rare (popmax 0.00698%, afr); Associated with glycogen storage disease IXa1.

What condition is associated with PHKA2 p.Pro28= (c.84C>T)?

PHKA2 p.Pro28= (c.84C>T) is associated with glycogen storage disease IXa1 (ClinVar).

How common is PHKA2 p.Pro28= (c.84C>T) in the general population?

PHKA2 p.Pro28= (c.84C>T) is very rare (popmax 0.00698%, afr) (gnomAD).

PHKA2 p.Pro28=

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.84C>T · rs149538323 · VCV2725904

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00698%, afr)

Conditions

glycogen storage disease IXa1

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 -11	GERP -4.4
Overall
CADD	0.01	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00698% African / African-American · 4/57,288 alleles

Filtering AF 0.00233% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0014%

Overall 0.00157% 19/1,208,972 alleles · very rare exomes 17/1,096,461 · genomes 2/112,511 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00698%	14,322
Remaining individualsnot grpmax-eligible	0.0042%	23,790
East Asian	0.00296%	33,773
Finnishnot grpmax-eligible	0.00219%	45,729
Admixed American	0.00218%	45,879
South Asian	0.00176%	56,877
European (non-Finnish)	0.00101%	99,418

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: PHKA2
Protein: p.Pro28=
Coding: c.84C>T
MANE Select: NM_000292
dbSNP: rs149538323
Type: single nucleotide variant
Location: chrX:18954407 (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 c.1325-2A>G Likely pathogenic ★★ same condition
PHKA2 c.2597+1G>A Pathogenic/Likely pathogenic ★★ same condition
PHKA2 c.537+2T>C Pathogenic/Likely pathogenic ★★ same condition
PHKA2 c.918+1G>A Pathogenic/Likely pathogenic ★★ same condition
PHKA2 p.Arg1111Ter Pathogenic ★★ same condition
PHKA2 p.Arg186Cys Pathogenic/Likely pathogenic ★★ same condition
PHKA2 p.Arg186His Likely pathogenic ★★ same condition
PHKA2 p.Arg295Cys 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/phka2-p-pro28 (accessed [today's date]).

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