CCDC22 p.Gln404=
c.1212G>A · VCV3390715
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.52 | donor loss · deltas |
|---|---|---|
| Pangolin | Δ0.72 | loss · gain 0.20 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 9.8 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 22.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CCDC22
- Protein
- p.Gln404=
- Coding
- c.1212G>A
- MANE Select
- NM_014008
- Type
- single nucleotide variant
- Location
- chrX:49248310 (GRCh38)
- Structure
- AlphaFold pLDDT 78.95 · 4 PDB
- Residue 404
- the 'sufficicient and required for interaction with ccdc93' region
Similar variants
- CCDC22 p.Ala463Gly Uncertain significance ★★ ⚠ same type
- CCDC22 p.Arg107Cys Uncertain significance ★★ ⚠ same type
- CCDC22 p.Arg128Gln Uncertain significance ★★ ⚠ same type
- CCDC22 p.Arg135Gln Uncertain significance ★★ ⚠ same type
- CCDC22 p.Arg148Cys Uncertain significance ★★ ⚠ same type
- CCDC22 p.Arg245Gln Uncertain significance ★★ ⚠ same type
- CCDC22 p.Arg257His Uncertain significance ★★ ⚠ same type
- CCDC22 p.Arg379Cys 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/ccdc22-p-gln404 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown