AGPAT2 p.Pro112=
c.336G>A · VCV4708076
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.005%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.6 | GERP -4.2 |
| Overall | ||
| CADD | 5.676 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.005%
Admixed American · 3/60,006 alleles
Filtering AF
0.00133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000668%
Overall
0.000806%
13/1,612,938 alleles · very rare
exomes 10/1,460,750 · genomes 3/152,188 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.005% | 20,002 |
| South Asian | 0.00329% | 30,358 |
| African / African-American | 0.00267% | 37,456 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,464 |
| European (non-Finnish) | 0.000339% | 294,998 |
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
- AGPAT2
- Protein
- p.Pro112=
- Coding
- c.336G>A
- MANE Select
- NM_006412
- Type
- single nucleotide variant
- Location
- chr9:136677117 (GRCh38)
- Gene constraint
- LOEUF 1.199 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 91.66
Similar variants
- AGPAT2 p.Pro112Leu Likely pathogenic ★ same residue
- AGPAT2 p.Pro112fs Pathogenic/Likely pathogenic ★★ same residue
- AGPAT2 c.492+1G>A Pathogenic/Likely pathogenic ★★ same type
- AGPAT2 c.493-1G>C Pathogenic/Likely pathogenic ★★ same type
- AGPAT2 c.493-2A>G Likely pathogenic ★★ same type
- AGPAT2 c.589-2A>G Pathogenic ★★ same type
- AGPAT2 c.662-2A>C Pathogenic/Likely pathogenic ★★ same type
- AGPAT2 p.Arg68Ter Pathogenic ★★ 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/agpat2-p-pro112 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown