ANAPC2 p.Ala664=
c.1992G>A · rs41317010 · VCV787588
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.323%, nfe)
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 -13 | GERP -3 |
| Overall | ||
| CADD | 0.089 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.323%
European (non-Finnish) · 3,811/1,179,614 alleles
Filtering AF
0.314%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.311%
Overall
0.275%
4,441/1,612,072 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.323% | 310 |
| Remaining individualsnot grpmax-eligible | 0.314% | 318 |
| African / African-American | 0.262% | 381 |
| Admixed American | 0.212% | 472 |
| Middle Eastern | 0.165% | 605 |
| Ashkenazi Jewishnot grpmax-eligible | 0.071% | 1,408 |
| South Asian | 0.066% | 1,516 |
| Finnishnot grpmax-eligible | 0.0271% | 3,686 |
| East Asian | 0.00446% | 22,430 |
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
- ANAPC2
- Protein
- p.Ala664=
- Coding
- c.1992G>A
- MANE Select
- NM_013366
- dbSNP
- rs41317010
- Type
- single nucleotide variant
- Location
- chr9:137175736 (GRCh38)
- Gene constraint
- LOEUF 0.482 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 79.44 · 23 PDB
- Residue 664
- the 'cullin homology' region; an α-helix
Similar variants
- ANAPC2 p.Tyr509= Benign ★★ same type
- ANAPC2 p.Ala36Val Uncertain significance ★ ⚠ same type
- ANAPC2 p.Ala380Asp Uncertain significance ★ ⚠ same type
- ANAPC2 p.Ala4Val Uncertain significance ★ ⚠ same type
- ANAPC2 p.Arg121Leu Uncertain significance ★ ⚠ same type
- ANAPC2 p.Arg210His Uncertain significance ★ ⚠ same type
- ANAPC2 p.Arg270Gln Uncertain significance ★ ⚠ same type
- ANAPC2 p.Arg270Trp 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/anapc2-p-ala664 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown