CCNF p.Val411=
c.1233G>A · rs111543933 · VCV3047555
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.405%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.20 | acceptor loss, 14 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -15 | GERP -3.2 |
| Overall | ||
| CADD | 0.034 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.405%
African / African-American · 304/75,062 alleles
Filtering AF
0.367%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.353%
Overall
0.0211%
341/1,613,842 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.405% | 247 |
| Admixed American | 0.0333% | 3,002 |
| Remaining individualsnot grpmax-eligible | 0.024% | 4,167 |
| East Asian | 0.00223% | 44,880 |
| European (non-Finnish) | 8.48e-05% | 1,179,912 |
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.Val411=
- Coding
- c.1233G>A
- MANE Select
- NM_001761
- dbSNP
- rs111543933
- Type
- single nucleotide variant
- Location
- chr16:2449296 (GRCh38)
- Gene constraint
- LOEUF 0.531 · pLI 0.70 (gnomAD)
- Structure
- AlphaFold pLDDT 72.34 · 1 PDB
- Residue 411
- an α-helix
Similar variants
- CCNF p.Ser621Gly Pathogenic/Likely pathogenic ★★ ⚠ same type
- CCNF p.Arg140Gln Uncertain significance ★★ ⚠ same type
- CCNF p.Arg24Lys Uncertain significance ★★ ⚠ same type
- CCNF p.Arg572Gln Uncertain significance ★★ ⚠ same type
- CCNF p.Gly254Ala Uncertain significance ★★ ⚠ same type
- CCNF p.Gly719Val Uncertain significance ★★ ⚠ same type
- CCNF c.1095-28A>G Benign ★★ same type
- CCNF c.1095-7G>A Benign ★★ 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-val411 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown