CDCA2 p.Lys533=
c.1599A>G · rs115925873 · VCV776299
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.74%, afr)
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 2.6 | GERP -2, phastCons 1 |
| Overall | ||
| CADD | 7.069 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.74%
African / African-American · 1,304/75,002 alleles
Filtering AF
1.66%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.63%
Overall
0.0912%
1,472/1,613,402 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.74% | 58 |
| Admixed American | 0.16% | 624 |
| Remaining individualsnot grpmax-eligible | 0.0944% | 1,059 |
| Middle Eastern | 0.0165% | 6,058 |
| European (non-Finnish) | 0.00102% | 98,315 |
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.Lys533=
- Coding
- c.1599A>G
- MANE Select
- NM_152562
- dbSNP
- rs115925873
- Type
- single nucleotide variant
- Location
- chr8:25488617 (GRCh38)
- Gene constraint
- LOEUF 0.84 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 46.61 · 4 PDB
Similar variants
- CDCA2 p.Val467Ile Uncertain significance ★★ ⚠ same type
- CDCA2 p.Lys754Thr Benign ★★ same type
- CDCA2 p.Ser291= 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
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-lys533 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown