CCDC22 p.Ser205=
c.615G>A · rs150796681 · VCV547081
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.252%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.33 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.20 | gain · loss 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -11 | GERP -2.8 |
| Overall | ||
| CADD | 0.455 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.252%
Middle Eastern · 11/4,357 alleles
Filtering AF
0.142%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.109%
Overall
0.0106%
128/1,203,047 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.252% | 396 |
| Remaining individualsnot grpmax-eligible | 0.0296% | 3,379 |
| South Asian | 0.0162% | 6,175 |
| European (non-Finnish) | 0.00953% | 10,488 |
| African / African-American | 0.007% | 14,286 |
| Admixed American | 0.00665% | 15,044 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00458% | 21,846 |
| Finnishnot grpmax-eligible | 0.00217% | 46,046 |
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
- CCDC22
- Protein
- p.Ser205=
- Coding
- c.615G>A
- MANE Select
- NM_014008
- dbSNP
- rs150796681
- Type
- single nucleotide variant
- Location
- chrX:49243363 (GRCh38)
- Structure
- AlphaFold pLDDT 78.95 · 4 PDB
- Residue 205
- the 'sufficicient and required for interaction with ccdc93' region; an α-helix; the 'sufficient for interaction with commd1' region
Similar variants
- CCDC22 p.Ser205Leu Uncertain significance ★ ⚠ same residue
- 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
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-ser205 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown