CCNQ p.Ser151=
c.453C>T · rs1557026101 · VCV509623
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00176%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.30 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.29 | gain · loss 0.08 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 0.19 | GERP -3.4, phastCons 0.93 |
| Overall | ||
| CADD | 5.82 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00176%
South Asian · 1/56,681 alleles
Overall
0.000182%
2/1,096,540 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00176% | 56,681 |
| European (non-Finnish) | 0.000112% | 894,871 |
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.Ser151=
- Coding
- c.453C>T
- MANE Select
- NM_152274
- dbSNP
- rs1557026101
- Type
- single nucleotide variant
- Location
- chrX:153592710 (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-ser151 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown