CDC16 p.Val256=
c.768A>G · VCV3829710
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00638%, nfe)
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 | GERP -0.55, phastCons 1 |
| Overall | ||
| CADD | 12.19 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00638%
European (non-Finnish) · 75/1,174,898 alleles
Filtering AF
0.00522%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00476%
Overall
0.00492%
79/1,607,266 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00638% | 15,665 |
| Remaining individualsnot grpmax-eligible | 0.00482% | 20,742 |
| Admixed American | 0.00168% | 59,602 |
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
- CDC16
- Protein
- p.Val256=
- Coding
- c.768A>G
- MANE Select
- NM_001078645
- Type
- single nucleotide variant
- Location
- chr13:114244890 (GRCh38)
- Gene constraint
- LOEUF 0.657 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 78.89 · 21 PDB
- Residue 256
- an α-helix
Similar variants
- CDC16 p.Ile132= Benign ★★ same type
- CDC16 p.Ala142Thr Uncertain significance ★ ⚠ same type
- CDC16 p.Ala319Thr Uncertain significance ★ ⚠ same type
- CDC16 p.Ala44Gly Uncertain significance ★ ⚠ same type
- CDC16 p.Ala479Ser Uncertain significance ★ ⚠ same type
- CDC16 p.Ala51Thr Uncertain significance ★ ⚠ same type
- CDC16 p.Ala536Ser Uncertain significance ★ ⚠ same type
- CDC16 p.Ala57Thr 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/cdc16-p-val256 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown