CCDC69 p.Leu294=
c.882C>T · rs374122246 · VCV2655944
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.15%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.379 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.87 | GERP -4.9 |
| Overall | ||
| CADD | 6.568 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.15%
Middle Eastern · 70/6,072 alleles
Filtering AF
0.936%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.857%
Overall
0.0175%
281/1,602,162 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.15% | 87 |
| South Asian | 0.0306% | 3,272 |
| Remaining individualsnot grpmax-eligible | 0.0306% | 3,272 |
| Admixed American | 0.0245% | 4,088 |
| European (non-Finnish) | 0.0121% | 8,280 |
| African / African-American | 0.00802% | 12,475 |
| East Asian | 0.00675% | 14,809 |
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
- CCDC69
- Protein
- p.Leu294=
- Coding
- c.882C>T
- MANE Select
- NM_015621
- dbSNP
- rs374122246
- Type
- single nucleotide variant
- Location
- chr5:151183446 (GRCh38)
- Gene constraint
- LOEUF 1.181 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.55
Similar variants
- CCDC69 p.Ala110Thr Uncertain significance ★ ⚠ same type
- CCDC69 p.Ala118Glu Uncertain significance ★ ⚠ same type
- CCDC69 p.Ala118Thr Uncertain significance ★ ⚠ same type
- CCDC69 p.Ala118Val Uncertain significance ★ ⚠ same type
- CCDC69 p.Ala75Val Uncertain significance ★ ⚠ same type
- CCDC69 p.Arg191Cys Uncertain significance ★ ⚠ same type
- CCDC69 p.Arg191His Uncertain significance ★ ⚠ same type
- CCDC69 p.Arg198Gln 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/ccdc69-p-leu294 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown