CCDC22 p.Pro191=
c.573A>C · rs782598913 · VCV733237
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0865%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.77 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.28 | gain · loss 0.10 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 0.72 | GERP -2.1, phastCons 0.95 |
| Overall | ||
| CADD | 21.5 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0865%
Admixed American · 39/45,106 alleles
Filtering AF
0.0649%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0575%
Overall
0.00499%
60/1,203,019 alleles · ultra-rare
exomes 49/1,090,603 · genomes 11/112,416 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0865% | 1,157 |
| Remaining individualsnot grpmax-eligible | 0.0359% | 2,782 |
| African / African-American | 0.00175% | 57,222 |
| European (non-Finnish) | 0.000337% | 297,113 |
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.Pro191=
- Coding
- c.573A>C
- MANE Select
- NM_014008
- dbSNP
- rs782598913
- Type
- single nucleotide variant
- Location
- chrX:49243321 (GRCh38)
- Structure
- AlphaFold pLDDT 78.95 · 4 PDB
- Residue 191
- the 'sufficicient and required for interaction with ccdc93' region; the 'sufficient for interaction with commd1' 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-pro191 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown