AGAP1 p.Pro837=
c.2511T>C · rs8178994 · VCV2114469
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 71%, 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 0.19 | GERP -0.64, phastCons 0.8 |
| Overall | ||
| CADD | 9.378 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
71%
African / African-American · 53,190/74,936 alleles
Filtering AF
70.5%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 70.3%
Overall
28.2%
455,484/1,613,830 alleles · common
exomes 397,832/1,461,782 · genomes 57,652/152,048 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 71% | 1 |
| South Asian | 36.2% | 3 |
| Finnishnot grpmax-eligible | 29.6% | 3 |
| Remaining individualsnot grpmax-eligible | 29% | 3 |
| Middle Eastern | 27.5% | 4 |
| European (non-Finnish) | 26% | 4 |
| Amishnot grpmax-eligible | 23% | 4 |
| East Asian | 20% | 5 |
| Ashkenazi Jewishnot grpmax-eligible | 18.4% | 5 |
| Admixed American | 14.9% | 7 |
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.Pro837=
- Coding
- c.2511T>C
- MANE Select
- NM_001037131
- dbSNP
- rs8178994
- Type
- single nucleotide variant
- Location
- chr2:236124059 (GRCh38)
- Gene constraint
- LOEUF 0.366 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.01 · 2 PDB
Similar variants
- AGAP1 p.Pro837Leu Uncertain significance ★★ ⚠ same residue
- AGAP1 p.Pro837Arg 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
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-pro837 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown