CCNQ p.Asp223=
c.669C>T · rs376050298 · VCV445928
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.083%, 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 0.072 | GERP -3.3, phastCons 0.77 |
| Overall | ||
| CADD | 3.963 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.083%
South Asian · 47/56,636 alleles
Filtering AF
0.0641%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0574%
Overall
0.0258%
310/1,199,793 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.083% | 1,205 |
| European (non-Finnish) | 0.0286% | 3,499 |
| African / African-American | 0.00873% | 11,448 |
| Remaining individualsnot grpmax-eligible | 0.00846% | 11,815 |
| Admixed American | 0.00218% | 45,889 |
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
- CCNQ
- Protein
- p.Asp223=
- Coding
- c.669C>T
- MANE Select
- NM_152274
- dbSNP
- rs376050298
- Type
- single nucleotide variant
- Location
- chrX:153588443 (GRCh38)
- Structure
- AlphaFold pLDDT 88.81
Similar variants
- CCNQ c.113-85T>C Benign ★★ same type
- CCNQ c.296+72C>T Benign ★★ same type
- CCNQ c.297-320A>G Benign ★★ same type
- CCNQ c.429+171C>T Benign ★★ same type
- CCNQ c.429+8C>T Benign ★★ same type
- CCNQ c.430-12G>A Benign/Likely benign ★★ same type
- CCNQ c.657+144C>T Benign ★★ same type
- CCNQ p.Ala209= Benign/Likely benign ★★ 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/ccnq-p-asp223 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown