CCNF p.Ala591=
c.1773G>A · rs118173479 · VCV717033
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.399%, mid)
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 -9.7 | GERP -3.1 |
| Overall | ||
| CADD | 2.289 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.399%
Middle Eastern · 24/6,022 alleles
Filtering AF
0.275%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.234%
Overall
0.116%
1,850/1,600,136 alleles · rare
exomes 1,697/1,447,770 · genomes 153/152,366 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.399% | 251 |
| Finnishnot grpmax-eligible | 0.236% | 423 |
| European (non-Finnish) | 0.122% | 819 |
| Remaining individualsnot grpmax-eligible | 0.12% | 835 |
| South Asian | 0.119% | 838 |
| Admixed American | 0.0837% | 1,195 |
| African / African-American | 0.02% | 4,988 |
| East Asian | 0.00225% | 44,368 |
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.Ala591=
- Coding
- c.1773G>A
- MANE Select
- NM_001761
- dbSNP
- rs118173479
- Type
- single nucleotide variant
- Location
- chr16:2455452 (GRCh38)
- Gene constraint
- LOEUF 0.531 · pLI 0.70 (gnomAD)
- Structure
- AlphaFold pLDDT 72.34 · 1 PDB
- Residue 591
- the 'disordered' region; the 'pest' region
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-ala591 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown