CDCA5 p.Thr105=
c.315A>G · rs35616304 · VCV716423
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.2%, afr)
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 · T>A here scores Δ0.47 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.6 | GERP -4.7 |
| Overall | ||
| CADD | 0.176 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.2%
African / African-American · 2,313/72,222 alleles
Filtering AF
3.09%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.05%
Overall
0.176%
2,716/1,542,330 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.2% | 31 |
| Admixed American | 0.272% | 368 |
| Remaining individualsnot grpmax-eligible | 0.235% | 426 |
| Middle Eastern | 0.0348% | 2,873 |
| European (non-Finnish) | 0.0115% | 8,677 |
| South Asian | 0.00246% | 40,730 |
| East Asian | 0.0023% | 43,470 |
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.Thr105=
- Coding
- c.315A>G
- MANE Select
- NM_080668
- dbSNP
- rs35616304
- Type
- single nucleotide variant
- Location
- chr11:65079716 (GRCh38)
- Gene constraint
- LOEUF 0.88 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.04
- Residue 105
- 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.Ala51Thr Uncertain significance ★ ⚠ same type
- CDCA5 p.Arg148Trp Uncertain significance ★ ⚠ same type
- CDCA5 p.Arg4Gly Uncertain significance ★ ⚠ same type
- CDCA5 p.Arg4Lys 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-thr105 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown