Is AGK p.Pro324= (c.972G>A) pathogenic?

AGK p.Pro324= (c.972G>A) is classified Likely benign in AGK (ClinVar, Single submitter, 1 submitter; last evaluated 2025-07-13). Ultra-rare (popmax 0.0333%, mid); Associated with Sengers syndrome.

What condition is associated with AGK p.Pro324= (c.972G>A)?

AGK p.Pro324= (c.972G>A) is associated with Sengers syndrome, cataract 38 (ClinVar).

How common is AGK p.Pro324= (c.972G>A) in the general population?

AGK p.Pro324= (c.972G>A) is ultra-rare (popmax 0.0333%, mid) (gnomAD).

AGK p.Pro324=

Q: How is Congenital cataract-hypertrophic cardiomyopathy-mitochondrial myopathy syndrome inherited?

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

c.972G>A · rs564152492 · VCV2083180

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0333%, mid)

Conditions

Sengers syndrome

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 0.99	GERP 1.7, phastCons 0.42
Overall
CADD	5.856	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0333% Middle Eastern · 2/6,014 alleles

Filtering AF 0.00586% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00244%

Overall 0.00254% 40/1,573,458 alleles · ultra-rare exomes 35/1,421,220 · genomes 5/152,238 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0333%	3,007
Admixed American	0.00746%	13,406
African / African-American	0.00402%	24,845
Remaining individualsnot grpmax-eligible	0.00327%	30,538
European (non-Finnish)	0.00242%	41,360
East Asian	0.00229%	43,580

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: AGK
Protein: p.Pro324=
Coding: c.972G>A
MANE Select: NM_018238
dbSNP: rs564152492
Type: single nucleotide variant
Location: chr7:141641905 (GRCh38)
Gene constraint: LOEUF 0.918 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 86.93 · 2 PDB
Residue 324: a UniProt-annotated variant site (in mtdps10)

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

Disease context

Sengers syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: cataract 38

For Congenital cataract-hypertrophic cardiomyopathy-mitochondrial myopathy syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

AGK p.Pro324Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
AGK c.1047-2A>T Pathogenic/Likely pathogenic ★★ same condition
AGK c.222-2A>C Likely pathogenic ★★ same condition
AGK c.297+2T>C Pathogenic ★★ same condition
AGK c.424-3C>G Pathogenic/Likely pathogenic ★★ same condition
AGK c.518+1G>A Pathogenic ★★ same condition
AGK p.Arg137Ter Pathogenic ★★ same condition
AGK p.Arg138Ter 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/agk-p-pro324 (accessed [today's date]).

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