AGAP1 p.Arg294=
c.880C>A · rs112968637 · VCV2039706
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.96%, 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 5.9 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 12.75 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.96%
African / African-American · 2,223/75,006 alleles
Filtering AF
2.86%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.82%
Overall
0.152%
2,453/1,614,116 alleles · low-frequency
exomes 1,214/1,461,890 · genomes 1,239/152,226 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.96% | 34 |
| Middle Eastern | 0.181% | 551 |
| Remaining individualsnot grpmax-eligible | 0.162% | 619 |
| Admixed American | 0.142% | 706 |
| South Asian | 0.00439% | 22,768 |
| European (non-Finnish) | 0.00246% | 40,691 |
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
- AGAP1
- Protein
- p.Arg294=
- Coding
- c.880C>A
- MANE Select
- NM_001037131
- dbSNP
- rs112968637
- Type
- single nucleotide variant
- Location
- chr2:235799445 (GRCh38)
- Gene constraint
- LOEUF 0.366 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.01 · 2 PDB
- Residue 294
- the 'disordered' region
Similar variants
- AGAP1 p.Arg294Leu Uncertain significance ★ ⚠ same residue
- AGAP1 p.Arg294Gln Likely benign ★ ⚠ same residue
- AGAP1 p.Ala418Ser Uncertain significance ★★ ⚠ same type
- AGAP1 p.Ala52Ser Uncertain significance ★★ ⚠ same type
- AGAP1 p.Ala570Gly Uncertain significance ★★ same type
- AGAP1 p.Ala809Ser Uncertain significance ★★ ⚠ same type
- AGAP1 p.Arg14Trp Uncertain significance ★★ ⚠ same type
- AGAP1 p.Arg313His 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/agap1-p-arg294 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown