CCNF p.Val104=
c.312G>A · VCV4684064
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.182%, 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 9.9 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 12.72 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.182%
Middle Eastern · 11/6,060 alleles
Filtering AF
0.102%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0787%
Overall
0.0374%
603/1,613,860 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.182% | 551 |
| South Asian | 0.0527% | 1,897 |
| European (non-Finnish) | 0.0424% | 2,360 |
| Admixed American | 0.035% | 2,857 |
| Remaining individualsnot grpmax-eligible | 0.0272% | 3,676 |
| East Asian | 0.00446% | 22,441 |
| African / African-American | 0.004% | 25,005 |
| Finnishnot grpmax-eligible | 0.00156% | 63,990 |
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.Val104=
- Coding
- c.312G>A
- MANE Select
- NM_001761
- Type
- single nucleotide variant
- Location
- chr16:2435839 (GRCh38)
- Gene constraint
- LOEUF 0.531 · pLI 0.70 (gnomAD)
- Structure
- AlphaFold pLDDT 72.34 · 1 PDB
- Residue 104
- 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-val104 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown