AGPAT2 p.Phe207=
c.621C>T · rs2490694593 · VCV2726442
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,537,968)
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 1.3 | GERP -4, phastCons 1 |
| Overall | ||
| CADD | 3.082 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,537,968). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- AGPAT2
- Protein
- p.Phe207=
- Coding
- c.621C>T
- MANE Select
- NM_006412
- dbSNP
- rs2490694593
- Type
- single nucleotide variant
- Location
- chr9:136674775 (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-phe207 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown