CCNF p.Tyr250=
c.750C>T · VCV3352136
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00659%, sas)
Conditions
1
CCNF-related disorder
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 · C>G here scores Δ0.37 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.1 | GERP -3.6 |
| Overall | ||
| CADD | 6.863 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00659%
South Asian · 6/91,078 alleles
Filtering AF
0.00286%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00195%
Overall
0.0028%
41/1,461,820 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00659% | 15,180 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,255 |
| European (non-Finnish) | 0.0028% | 35,757 |
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
- CCNF
- Protein
- p.Tyr250=
- Coding
- c.750C>T
- MANE Select
- NM_001761
- Type
- single nucleotide variant
- Location
- chr16:2439799 (GRCh38)
- Gene constraint
- LOEUF 0.531 · pLI 0.70 (gnomAD)
- Structure
- AlphaFold pLDDT 72.34 · 1 PDB
- Residue 250
- an α-helix
Disease context
CCNF-related disorder
Similar variants
- CCNF c.347-4G>A Likely benign same condition
- CCNF p.Ala145= Likely benign same condition
- CCNF p.Ala74Thr Benign same condition
- CCNF p.Arg349= Likely benign same condition
- CCNF p.Leu352= Likely benign same condition
- CCNF p.Leu531Arg Likely benign ⚠ same condition
- CCNF p.Ser704= Likely benign same condition
- CCNF p.Ser621Gly Pathogenic/Likely pathogenic ★★ ⚠ 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/ccnf-p-tyr250 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown