AGAP2 p.Pro108Ser
c.322C>T · rs1454671196 · VCV2495812
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00148%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.054 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 9.3 | GERP -0.24, phastCons 1 |
| Regional constraint | o/e 0.90 | unconstrained · MANE · 6,676 bp · p 0.0015 · regional, not allelic |
| Overall | ||
| CADD | 22.3 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00148%
European (non-Finnish) · 16/1,084,066 alleles
Filtering AF
0.000874%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000707%
Overall
0.00115%
16/1,391,570 alleles · very rare
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
- AGAP2
- Protein
- p.Pro108Ser
- Coding
- c.322C>T
- MANE Select
- NM_001122772
- dbSNP
- rs1454671196
- Type
- single nucleotide variant
- Location
- chr12:57737925 (GRCh38)
- Gene constraint
- LOEUF 0.414 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 60.04 · 3 PDB
- Residue 108
- the 'disordered' region
Similar variants
- AGAP2 p.Leu210Gln Uncertain significance ★★ same type
- AGAP2 p.Val527= Benign ★★ same type
- AGAP2 p.Ala1045Glu Uncertain significance ★ same type
- AGAP2 p.Ala1156Thr Uncertain significance ★ same type
- AGAP2 p.Ala1161Val Uncertain significance ★ same type
- AGAP2 p.Ala116Asp Uncertain significance ★ same type
- AGAP2 p.Ala228Val Uncertain significance ★ same type
- AGAP2 p.Ala237Thr 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/agap2-p-pro108ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown