CDCA5 p.Pro120=
c.360T>A · rs150704124 · VCV729058
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.852%, amr)
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 -3.6 | GERP -4.8 |
| Overall | ||
| CADD | 0.745 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.852%
Admixed American · 497/58,346 alleles
Filtering AF
0.79%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.765%
Overall
0.0367%
588/1,601,142 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.852% | 117 |
| Remaining individualsnot grpmax-eligible | 0.0533% | 1,874 |
| South Asian | 0.0435% | 2,301 |
| African / African-American | 0.0215% | 4,661 |
| European (non-Finnish) | 0.000256% | 390,848 |
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
- CDCA5
- Protein
- p.Pro120=
- Coding
- c.360T>A
- MANE Select
- NM_080668
- dbSNP
- rs150704124
- Type
- single nucleotide variant
- Location
- chr11:65079671 (GRCh38)
- Gene constraint
- LOEUF 0.88 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.04
- Residue 120
- the 'disordered' region
Similar variants
- CDCA5 p.Pro120Arg Uncertain significance ★ ⚠ same residue
- CDCA5 p.Glu123Lys Benign ★★ same type
- CDCA5 p.Gly173= Benign ★★ same type
- CDCA5 p.Gly179Arg Benign ★★ same type
- CDCA5 p.Thr105= Benign ★★ same type
- CDCA5 p.Ala51Thr Uncertain significance ★ ⚠ same type
- CDCA5 p.Arg148Trp Uncertain significance ★ same type
- CDCA5 p.Arg4Gly 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/cdca5-p-pro120 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown