AGAP2 p.Val527=
c.1581G>A · rs115767833 · VCV725324
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.782%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.019 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.8 | GERP -3, phastCons 1 |
| Overall | ||
| CADD | 12.01 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.782%
African / African-American · 587/75,032 alleles
Filtering AF
0.73%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.709%
Overall
0.0428%
691/1,614,088 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.782% | 128 |
| Middle Eastern | 0.165% | 606 |
| Admixed American | 0.0566% | 1,765 |
| Remaining individualsnot grpmax-eligible | 0.0496% | 2,016 |
| South Asian | 0.00439% | 22,771 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
| European (non-Finnish) | 0.00203% | 49,168 |
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
- AGAP2
- Protein
- p.Val527=
- Coding
- c.1581G>A
- MANE Select
- NM_001122772
- dbSNP
- rs115767833
- Type
- single nucleotide variant
- Location
- chr12:57732948 (GRCh38)
- Gene constraint
- LOEUF 0.414 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 60.04 · 3 PDB
- Residue 527
- the gld domain; the 'g domain' region
Similar variants
- AGAP2 p.Leu210Gln Uncertain significance ★★ same type
- AGAP2 p.Ala1045Glu Uncertain significance ★ same type
- AGAP2 p.Ala1156Thr Uncertain significance ★ same type
- AGAP2 p.Ala1161Val Uncertain significance ★ same type
- AGAP2 p.Ala116Asp Uncertain significance ★ same type
- AGAP2 p.Ala228Val Uncertain significance ★ same type
- AGAP2 p.Ala237Thr Uncertain significance ★ same type
- AGAP2 p.Ala260Asp 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/agap2-p-val527 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown