CCNQ p.Ala66=
c.198C>T · VCV3711861
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.085%, amr)
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 2.3 | GERP -0.42, phastCons 1 |
| Overall | ||
| CADD | 6.769 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.085%
Admixed American · 39/45,891 alleles
Filtering AF
0.0638%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0565%
Overall
0.0033%
40/1,210,975 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.085% | 1,177 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,611 |
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.Ala66=
- Coding
- c.198C>T
- MANE Select
- NM_152274
- Type
- single nucleotide variant
- Location
- chrX:153596102 (GRCh38)
- Structure
- AlphaFold pLDDT 88.81
Similar variants
- CCNQ p.Ala66fs Likely pathogenic ★ same residue
- 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
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-ala66 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown