CCNF p.Leu352=
c.1056C>T · rs2141824569 · VCV3044570
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000169%, nfe)
Conditions
1
CCNF-related disorder
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 -1.4 | GERP -3.1 |
| Overall | ||
| CADD | 3.014 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000169%
European (non-Finnish) · 2/1,180,018 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000137%
2/1,461,328 alleles · very rare
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.Leu352=
- Coding
- c.1056C>T
- MANE Select
- NM_001761
- dbSNP
- rs2141824569
- Type
- single nucleotide variant
- Location
- chr16:2445584 (GRCh38)
- Gene constraint
- LOEUF 0.531 · pLI 0.70 (gnomAD)
- Structure
- AlphaFold pLDDT 72.34 · 1 PDB
- Residue 352
- the cyclin n-terminal domain; 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.Leu531Arg Likely benign ⚠ same condition
- CCNF p.Ser704= Likely benign same condition
- CCNF p.Tyr250= 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-leu352 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown