Is AGMO p.Pro302Ser (c.904C>T) pathogenic?

AGMO p.Pro302Ser (c.904C>T) is classified Uncertain significance in AGMO (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-02-14). AlphaMissense: likely pathogenic (0.8828); Absent from gnomAD v4.1; Associated with AGMO-related disorder.

What condition is associated with AGMO p.Pro302Ser (c.904C>T)?

AGMO p.Pro302Ser (c.904C>T) is associated with AGMO-related disorder (ClinVar).

How common is AGMO p.Pro302Ser (c.904C>T) in the general population?

AGMO p.Pro302Ser (c.904C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about AGMO p.Pro302Ser (c.904C>T)?

AlphaMissense predicts likely pathogenic (score 0.8828) — an in-silico prediction, not a clinical call.

AGMO p.Pro302Ser

c.904C>T · rs1783962073 · VCV3044878

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8828 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

AGMO-related disorder

Computational evidence

Protein change
AlphaMissense	0.8828	likely pathogenic
REVEL	0.736	pathogenic-leaning
SaProt	LLR -10.23	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.7	GERP 1.6, phastCons 1
Regional constraint	o/e 1.45	unconstrained · MANE · 361 kb · p 3.8e-25 · regional, not allelic
Overall
CADD	26.5	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: AGMO
Protein: p.Pro302Ser
Coding: c.904C>T
MANE Select: NM_001004320
dbSNP: rs1783962073
Type: single nucleotide variant
Location: chr7:15387459 (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

Disease context

AGMO-related disorder

Similar variants

AGMO p.Pro302Leu Uncertain significance ★ ⚠ same residue
AGMO p.Asn207Lys Uncertain significance ★ ⚠ same condition
AGMO p.Leu412Ile Uncertain significance ★ ⚠ same condition
AGMO p.Pro264Ser Uncertain significance ★ ⚠ same condition
AGMO p.Ser219Cys Uncertain significance ⚠ same condition
AGMO c.1074+10A>G Likely benign same condition
AGMO p.His408= Likely benign same condition
AGMO p.Leu395Val Benign 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/agmo-p-pro302ser (accessed [today's date]).

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