AGAP1 p.Pro70=
c.210G>A · rs8178995 · VCV2003469
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 24.6%, afr) — too common for a highly-penetrant pathogenic allele
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 -7 | GERP -4.4 |
| Overall | ||
| CADD | 5.19 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
24.6%
African / African-American · 18,411/74,914 alleles
Filtering AF
24.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 24.2%
Overall
1.34%
21,705/1,613,930 alleles · common
exomes 11,017/1,461,826 · genomes 10,688/152,104 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 24.6% | 4 |
| Remaining individualsnot grpmax-eligible | 1.81% | 55 |
| Admixed American | 1.77% | 56 |
| Middle Eastern | 1.25% | 80 |
| Ashkenazi Jewishnot grpmax-eligible | 0.588% | 170 |
| European (non-Finnish) | 0.0669% | 1,496 |
| South Asian | 0.0582% | 1,718 |
| Finnishnot grpmax-eligible | 0.00625% | 16,000 |
| East Asian | 0.00446% | 22,428 |
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.Pro70=
- Coding
- c.210G>A
- MANE Select
- NM_001037131
- dbSNP
- rs8178995
- Type
- single nucleotide variant
- Location
- chr2:235709225 (GRCh38)
- Gene constraint
- LOEUF 0.366 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.01 · 2 PDB
- Residue 70
- the gld domain; the 'small gtpase-like' region
Similar variants
- AGAP1 p.Pro70Leu 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-pro70 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown