AGAP1 p.Ile190=
c.570C>T · rs576969179 · VCV2893966
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.055%, 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 -5 | GERP -5.6 |
| Overall | ||
| CADD | 8.294 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.055%
Admixed American · 33/60,028 alleles
Filtering AF
0.0402%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0351%
Overall
0.0031%
50/1,614,176 alleles · ultra-rare
exomes 40/1,461,878 · genomes 10/152,298 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.055% | 1,819 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,627 |
| African / African-American | 0.004% | 25,012 |
| South Asian | 0.0011% | 91,072 |
| European (non-Finnish) | 0.000763% | 131,116 |
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.Ile190=
- Coding
- c.570C>T
- MANE Select
- NM_001037131
- dbSNP
- rs576969179
- Type
- single nucleotide variant
- Location
- chr2:235750385 (GRCh38)
- Gene constraint
- LOEUF 0.366 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.01 · 2 PDB
- Residue 190
- the gld domain; the 'small gtpase-like' region
Similar variants
- AGAP1 p.Ile190Val Uncertain significance ★ ⚠ 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
- AGAP1 p.Arg696Trp 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-ile190 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown