CCDC80 p.Ala613=
c.1839C>G · rs142765055 · VCV3234333
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.098%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.011 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -2.2 | GERP -5.3 |
| Overall | ||
| CADD | 0.233 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.098%
African / African-American · 73/74,474 alleles
Filtering AF
0.0799%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0732%
Overall
0.00578%
93/1,609,418 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.098% | 1,020 |
| East Asian | 0.0356% | 2,805 |
| Remaining individualsnot grpmax-eligible | 0.00642% | 15,572 |
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.Ala613=
- Coding
- c.1839C>G
- MANE Select
- NM_199511
- dbSNP
- rs142765055
- Type
- single nucleotide variant
- Location
- chr3:112638067 (GRCh38)
- Gene constraint
- LOEUF 0.749 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 62.51
Similar variants
- CCDC80 p.Ala613Thr Likely benign ★ 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-ala613 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown