CCDC22 p.Ser158=
c.474G>A · rs369264021 · VCV730843
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.47%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -8.9 | GERP -2.8 |
| Overall | ||
| CADD | 0.009 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.47%
South Asian · 831/56,591 alleles
Filtering AF
1.39%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.35%
Overall
0.0873%
1,055/1,209,038 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.47% | 68 |
| Middle Eastern | 0.207% | 484 |
| Remaining individualsnot grpmax-eligible | 0.105% | 951 |
| East Asian | 0.0178% | 5,625 |
| European (non-Finnish) | 0.0167% | 6,002 |
| Admixed American | 0.0109% | 9,164 |
| African / African-American | 0.00698% | 14,333 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00455% | 21,983 |
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.Ser158=
- Coding
- c.474G>A
- MANE Select
- NM_014008
- dbSNP
- rs369264021
- Type
- single nucleotide variant
- Location
- chrX:49243123 (GRCh38)
- Structure
- AlphaFold pLDDT 78.95 · 4 PDB
- Residue 158
- the 'sufficicient and required for interaction with ccdc93' region; the 'sufficient for interaction with commd1' region
Similar variants
- CCDC22 p.Ser158Leu Likely benign ★★ 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-ser158 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown