AGMO p.Ala143=
c.429C>T · rs116358801 · VCV790038
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.74%, afr)
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 -0.084 | GERP -0.98, phastCons 0.008 |
| Overall | ||
| CADD | 5.209 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.74%
African / African-American · 1,303/74,716 alleles
Filtering AF
1.67%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.63%
Overall
0.104%
1,677/1,610,648 alleles · low-frequency
exomes 914/1,459,040 · genomes 763/151,608 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.74% | 57 |
| Ashkenazi Jewishnot grpmax-eligible | 0.535% | 187 |
| Remaining individualsnot grpmax-eligible | 0.164% | 611 |
| Admixed American | 0.087% | 1,149 |
| Middle Eastern | 0.0826% | 1,210 |
| South Asian | 0.00771% | 12,975 |
| European (non-Finnish) | 0.00416% | 24,038 |
| East Asian | 0.00223% | 44,744 |
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.Ala143=
- Coding
- c.429C>T
- MANE Select
- NM_001004320
- dbSNP
- rs116358801
- Type
- single nucleotide variant
- Location
- chr7:15431089 (GRCh38)
- Gene constraint
- LOEUF 1.561 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.90
- Residue 143
- 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-ala143 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown