AGAP1 p.Thr319=
c.957C>T · rs2292708 · VCV2003470
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 47%, amr) — 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 | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -10 | GERP -4.1 |
| Overall | ||
| CADD | 3.79 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
47%
Admixed American · 28,160/59,962 alleles
Filtering AF
46.5%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 46.3%
Overall
27.9%
450,413/1,613,210 alleles · common
exomes 415,280/1,461,136 · genomes 35,133/152,074 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 47% | 2 |
| European (non-Finnish) | 29.7% | 3 |
| Finnishnot grpmax-eligible | 29.2% | 3 |
| Remaining individualsnot grpmax-eligible | 26.2% | 4 |
| Ashkenazi Jewishnot grpmax-eligible | 24.6% | 4 |
| East Asian | 24.4% | 4 |
| Amishnot grpmax-eligible | 23.8% | 4 |
| Middle Eastern | 17.7% | 6 |
| South Asian | 13.8% | 7 |
| African / African-American | 5.9% | 17 |
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.Thr319=
- Coding
- c.957C>T
- MANE Select
- NM_001037131
- dbSNP
- rs2292708
- Type
- single nucleotide variant
- Location
- chr2:235799522 (GRCh38)
- Gene constraint
- LOEUF 0.366 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.01 · 2 PDB
- Residue 319
- the 'disordered' region
Similar variants
- 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
- AGAP1 p.Arg770Cys 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-thr319 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown