CCNO p.Gln96=
c.288G>A · rs1580412048 · VCV761081
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 2.7 | GERP 0.83, phastCons 1 |
| Overall | ||
| CADD | 13.67 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CCNO
- Protein
- p.Gln96=
- Coding
- c.288G>A
- MANE Select
- NM_021147
- dbSNP
- rs1580412048
- Type
- single nucleotide variant
- Location
- chr5:55233236 (GRCh38)
- Gene constraint
- LOEUF 1.698 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.06
Similar variants
- CCNO p.Gln96Ter Likely pathogenic ★ same residue
- CCNO p.Gln103Ter Pathogenic ★★ same type
- CCNO p.Ala14Ser Uncertain significance ★★ ⚠ same type
- CCNO p.Ala202Val Uncertain significance ★★ ⚠ same type
- CCNO p.Ala230Thr Uncertain significance ★★ ⚠ same type
- CCNO p.Ala258Gly Uncertain significance ★★ ⚠ same type
- CCNO p.Arg124Leu Uncertain significance ★★ ⚠ same type
- CCNO p.Arg124Trp 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/ccno-p-gln96 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown