CCNQ p.Ala209=
c.627C>T · rs139186601 · VCV702552
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.73%, 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 -0.76 | GERP -3.1 |
| Overall | ||
| CADD | 0.339 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.73%
South Asian · 1,555/56,908 alleles
Filtering AF
2.62%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.57%
Overall
0.197%
2,391/1,211,231 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 2.73% | 37 |
| Middle Eastern | 0.759% | 132 |
| Remaining individualsnot grpmax-eligible | 0.189% | 529 |
| European (non-Finnish) | 0.0772% | 1,296 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0227% | 4,409 |
| Finnishnot grpmax-eligible | 0.0193% | 5,193 |
| East Asian | 0.00888% | 11,259 |
| African / African-American | 0.0052% | 19,247 |
| Admixed American | 0.00434% | 23,015 |
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.Ala209=
- Coding
- c.627C>T
- MANE Select
- NM_152274
- dbSNP
- rs139186601
- Type
- single nucleotide variant
- Location
- chrX:153592536 (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.Arg113His 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-ala209 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown