CCDC80 p.Tyr163=
c.489C>T · rs16859892 · VCV780880
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.56%, afr)
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 8.6 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 11.48 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.56%
African / African-American · 3,421/75,036 alleles
Filtering AF
4.43%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.38%
Overall
0.24%
3,867/1,614,190 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.56% | 22 |
| Admixed American | 0.302% | 332 |
| Remaining individualsnot grpmax-eligible | 0.294% | 340 |
| Middle Eastern | 0.198% | 505 |
| South Asian | 0.0187% | 5,358 |
| European (non-Finnish) | 0.00441% | 22,693 |
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.Tyr163=
- Coding
- c.489C>T
- MANE Select
- NM_199511
- dbSNP
- rs16859892
- Type
- single nucleotide variant
- Location
- chr3:112639417 (GRCh38)
- Gene constraint
- LOEUF 0.749 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 62.51
Similar variants
- CCDC80 p.Ala805Val Benign ★★ ⚠ same type
- CCDC80 p.His473Tyr 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
- CCDC80 p.Ala125Pro Uncertain significance ★ ⚠ same type
- CCDC80 p.Ala318Pro 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-tyr163 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown