AGAP1 p.Glu829=
c.2487G>A · rs143254472 · VCV731514
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.174%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.132 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 4.3 | GERP 0.47, phastCons 1 |
| Overall | ||
| CADD | 6.111 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.174%
European (non-Finnish) · 2,048/1,180,000 alleles
Filtering AF
0.167%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.165%
Overall
0.148%
2,382/1,614,082 alleles · rare
exomes 2,187/1,461,790 · genomes 195/152,292 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.174% | 576 |
| Admixed American | 0.162% | 619 |
| Remaining individualsnot grpmax-eligible | 0.146% | 687 |
| Ashkenazi Jewishnot grpmax-eligible | 0.142% | 705 |
| Middle Eastern | 0.115% | 866 |
| Amishnot grpmax-eligible | 0.11% | 912 |
| South Asian | 0.0593% | 1,687 |
| African / African-American | 0.0426% | 2,345 |
| Finnishnot grpmax-eligible | 0.0156% | 6,399 |
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.Glu829=
- Coding
- c.2487G>A
- MANE Select
- NM_001037131
- dbSNP
- rs143254472
- Type
- single nucleotide variant
- Location
- chr2:236124035 (GRCh38)
- Gene constraint
- LOEUF 0.366 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.01 · 2 PDB
- Residue 829
- a UniProt-annotated variant site (in)
Similar variants
- AGAP1 p.Glu829Lys 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-glu829 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown