CCDC88A p.Pro27His
c.80C>A · rs762723160 · VCV2104885
Computational evidence
| Protein change | ||
| AlphaMissense | 0.1084 | likely benign |
|---|---|---|
| REVEL | 0.198 | benign-leaning |
| SaProt | LLR -7.83 | tolerated |
| ⇒ AlphaMissense, REVEL and SaProt all call this tolerated. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 9.8 | GERP 1.8, phastCons 1 |
| Regional constraint | o/e 0.82 | unconstrained · MANE · 209 bp · p 0.23 · regional, not allelic |
| Overall | ||
| CADD | 25.1 | PHRED · no single calibrated threshold — expert panels disagree |
ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
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
- CCDC88A
- Protein
- p.Pro27His
- Coding
- c.80C>A
- MANE Select
- NM_001365480
- dbSNP
- rs762723160
- Type
- single nucleotide variant
- Location
- chr2:55418900 (GRCh38)
- Gene constraint
- LOEUF 0.25 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 67.09 · 1 PDB
- Residue 27
- the calponin-homology (ch) domain
Similar variants
- CCDC88A p.Pro27Ser Uncertain significance ★ ⚠ same residue
- CCDC88A p.Ala1536Thr Uncertain significance ★★ ⚠ same type
- CCDC88A p.Ala155Val Uncertain significance ★★ ⚠ same type
- CCDC88A p.Ala158Thr Uncertain significance ★★ ⚠ same type
- CCDC88A p.Ala1770Val Uncertain significance ★★ ⚠ same type
- CCDC88A p.Ala194Thr Uncertain significance ★★ ⚠ same type
- CCDC88A p.Ala72Thr Uncertain significance ★★ ⚠ same type
- CCDC88A p.Ala845Gly 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/ccdc88a-p-pro27his (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown