Is AGMO p.Glu324fs (c.969del) pathogenic?

AGMO p.Glu324fs (c.969del) is classified Pathogenic in AGMO (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-10). Very rare (popmax 0.00273%, nfe).

How common is AGMO p.Glu324fs (c.969del) in the general population?

AGMO p.Glu324fs (c.969del) is very rare (popmax 0.00273%, nfe) (gnomAD).

AGMO p.Glu324fs

c.969del · VCV3340295

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00273%, nfe)

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 10 of 13
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 5.8	GERP 1.4, phastCons 1
Overall
CADD	22.8	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00273% European (non-Finnish) · 32/1,173,182 alleles

Filtering AF 0.00197% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00169%

Overall 0.00205% 33/1,606,034 alleles · very rare exomes 31/1,453,890 · genomes 2/152,144 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00273%	36,662
Remaining individualsnot grpmax-eligible	0.00161%	62,228

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: AGMO
Protein: p.Glu324fs
Coding: c.969del
MANE Select: NM_001004320
Type: Deletion
Location: chr7:15385551 (GRCh38)
Gene constraint: LOEUF 1.561 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.90

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

Similar variants

AGMO p.Glu324Ter Uncertain significance ★ same residue
AGMO p.Tyr236del Likely pathogenic ★★ same type
AGMO c.957_957+18del Likely pathogenic ★ same type
AGMO c.1263+8del Uncertain significance ★ same type
AGMO c.676+5_676+11del Uncertain significance ★ same type
AGMO c.677-3_677-2del Uncertain significance ★ same type
AGMO p.Gln362fs Uncertain significance ★ same type
AGMO p.Leu367del Uncertain significance ★ same type

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/agmo-p-glu324fs (accessed [today's date]).

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