AGMO p.Phe173=
c.519C>T · rs758015123 · VCV716876
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0938%, mid)
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 3.7 | GERP 0.9, phastCons 1 |
| Overall | ||
| CADD | 8.488 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0938%
Middle Eastern · 5/5,330 alleles
Filtering AF
0.0369%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.024%
Overall
0.00402%
62/1,540,622 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0938% | 1,066 |
| Admixed American | 0.0246% | 4,059 |
| African / African-American | 0.0157% | 6,370 |
| Remaining individualsnot grpmax-eligible | 0.00673% | 14,857 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00363% | 27,568 |
| European (non-Finnish) | 0.00262% | 38,187 |
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.Phe173=
- Coding
- c.519C>T
- MANE Select
- NM_001004320
- dbSNP
- rs758015123
- Type
- single nucleotide variant
- Location
- chr7:15418648 (GRCh38)
- Gene constraint
- LOEUF 1.561 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.90
- Residue 173
- the fatty acid hydroxylase domain
Similar variants
- AGMO p.Arg133Cys Uncertain significance ★★ ⚠ same type
- AGMO p.Arg83Gln Uncertain significance ★★ ⚠ same type
- AGMO p.Gly238Cys Uncertain significance ★★ ⚠ same type
- AGMO p.Gly322Ser Uncertain significance ★★ ⚠ same type
- AGMO p.Ile281Val Uncertain significance ★★ ⚠ same type
- AGMO p.Leu213Val Uncertain significance ★★ ⚠ same type
- AGMO p.Lys234Arg Uncertain significance ★★ ⚠ same type
- AGMO p.Lys24Glu 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-phe173 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown