AGPAT2 p.Pro5=
c.15G>A · VCV4727781
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00118%, sas)
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 -0.92 | GERP -2.3, phastCons 0.008 |
| Overall | ||
| CADD | 8.907 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00118%
South Asian · 1/84,906 alleles
Overall
0.000129%
2/1,546,714 alleles · very rare
exomes 2/1,394,500 · genomes 0/152,214 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00118% | 84,906 |
| European (non-Finnish) | 8.66e-05% | 1,154,692 |
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.Pro5=
- Coding
- c.15G>A
- MANE Select
- NM_006412
- Type
- single nucleotide variant
- Location
- chr9:136687343 (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 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
- AGPAT2 p.Gln264Ter Likely pathogenic ★★ same type
- AGPAT2 p.Glu172Lys Pathogenic/Likely 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-pro5 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown