CDCA5 p.Lys218=
c.654G>A · rs149256940 · VCV709975
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.358%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.271 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 3.3 | GERP 0.078, phastCons 1 |
| Overall | ||
| CADD | 11.42 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.358%
European (non-Finnish) · 4,222/1,180,008 alleles
Filtering AF
0.349%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.345%
Overall
0.272%
4,393/1,614,106 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.358% | 279 |
| Remaining individualsnot grpmax-eligible | 0.138% | 727 |
| African / African-American | 0.064% | 1,563 |
| Finnishnot grpmax-eligible | 0.0328% | 3,049 |
| Admixed American | 0.0267% | 3,751 |
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.Lys218=
- Coding
- c.654G>A
- MANE Select
- NM_080668
- dbSNP
- rs149256940
- Type
- single nucleotide variant
- Location
- chr11:65079377 (GRCh38)
- Gene constraint
- LOEUF 0.88 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.04
- Residue 218
- the 'disordered' region
Similar variants
- CDCA5 p.Glu123Lys Benign ★★ same type
- CDCA5 p.Gly173= Benign ★★ same type
- CDCA5 p.Gly179Arg Benign ★★ same type
- CDCA5 p.Pro120= 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-lys218 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown