CDCA2 p.Ser291=
c.873G>A · rs112148375 · VCV768231
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 9.72%, 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 | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.45 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.6 | GERP -4.8 |
| Overall | ||
| CADD | 0.441 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
9.72%
African / African-American · 7,285/74,974 alleles
Filtering AF
9.53%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9.45%
Overall
0.516%
8,336/1,614,012 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 9.72% | 10 |
| Remaining individualsnot grpmax-eligible | 0.718% | 139 |
| Admixed American | 0.67% | 149 |
| Middle Eastern | 0.347% | 289 |
| South Asian | 0.022% | 4,554 |
| European (non-Finnish) | 0.0131% | 7,613 |
| East Asian | 0.00669% | 14,958 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,604 |
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
- CDCA2
- Protein
- p.Ser291=
- Coding
- c.873G>A
- MANE Select
- NM_152562
- dbSNP
- rs112148375
- Type
- single nucleotide variant
- Location
- chr8:25479965 (GRCh38)
- Gene constraint
- LOEUF 0.84 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 46.61 · 4 PDB
- Residue 291
- a modified residue (phosphoserine)
Similar variants
- CDCA2 p.Val467Ile Uncertain significance ★★ ⚠ same type
- CDCA2 p.Lys754Thr Benign ★★ same type
- CDCA2 p.Thr50Ile Benign ★★ same type
- CDCA2 p.Ala187Thr Uncertain significance ★ ⚠ same type
- CDCA2 p.Ala217Val Uncertain significance ★ ⚠ same type
- CDCA2 p.Ala23Val Uncertain significance ★ ⚠ same type
- CDCA2 p.Ala92Gly Uncertain significance ★ ⚠ same type
- CDCA2 p.Arg106His 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/cdca2-p-ser291 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown