CCDC80 p.Arg467=
c.1401C>T · rs760782964 · VCV2654033
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0329%, 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 2.6 | GERP 0.95, phastCons 1 |
| Overall | ||
| CADD | 10.66 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0329%
Middle Eastern · 2/6,084 alleles
Filtering AF
0.0058%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00241%
Overall
0.0013%
21/1,613,928 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0329% | 3,042 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,621 |
| Admixed American | 0.00167% | 59,986 |
| European (non-Finnish) | 0.00119% | 84,288 |
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
- CCDC80
- Protein
- p.Arg467=
- Coding
- c.1401C>T
- MANE Select
- NM_199511
- dbSNP
- rs760782964
- Type
- single nucleotide variant
- Location
- chr3:112638505 (GRCh38)
- Gene constraint
- LOEUF 0.749 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 62.51
- Residue 467
- the 'disordered' region
Similar variants
- CCDC80 p.Arg467His Uncertain significance ★ ⚠ same residue
- CCDC80 p.Ala805Val Benign ★★ ⚠ same type
- CCDC80 p.His473Tyr Benign ★★ same type
- CCDC80 p.Tyr163= Benign ★★ same type
- CCDC80 p.Tyr938His Likely benign ★★ ⚠ same type
- CCDC80 p.Ala101Val Uncertain significance ★ ⚠ same type
- CCDC80 p.Ala110Pro Uncertain significance ★ ⚠ same type
- CCDC80 p.Ala110Ser Uncertain significance ★ ⚠ 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/ccdc80-p-arg467 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown