AGMAT p.Pro324=
c.972G>A · VCV4251892
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0134%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.058 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -5.6 | GERP -5.5 |
| Overall | ||
| CADD | 1.786 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0134%
East Asian · 6/44,872 alleles
Filtering AF
0.00681%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00633%
Overall
0.00669%
108/1,613,500 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0134% | 7,479 |
| European (non-Finnish) | 0.00814% | 12,287 |
| South Asian | 0.00439% | 22,766 |
| Admixed American | 0.00167% | 59,998 |
| Finnishnot grpmax-eligible | 0.00156% | 63,992 |
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
- AGMAT
- Protein
- p.Pro324=
- Coding
- c.972G>A
- MANE Select
- NM_024758
- Type
- single nucleotide variant
- Location
- chr1:15574770 (GRCh38)
- Gene constraint
- LOEUF 1.712 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.12
Similar variants
- AGMAT p.Pro324Gln Uncertain significance ★ ⚠ same residue
- AGMAT p.Thr229Met Benign ★★ same type
- AGMAT p.Thr351= Benign ★★ same type
- AGMAT p.Ala10Ser Uncertain significance ★ ⚠ same type
- AGMAT p.Ala113Asp Uncertain significance ★ same type
- AGMAT p.Ala186Val Uncertain significance ★ ⚠ same type
- AGMAT p.Ala285Val Uncertain significance ★ ⚠ same type
- AGMAT p.Ala335Val 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/agmat-p-pro324 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown