CELSR3 p.Arg2886Pro
c.8657G>C · VCV4225446
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
likely pathogenic
0.6686 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| AlphaMissense | 0.6686 | likely pathogenic |
|---|---|---|
| REVEL | 0.572 | indeterminate |
| SaProt | — | not scored · why |
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.27 · evaluated, not missing |
| Pangolin | Δ0.21 | loss · gain 0.02 · SpliceAI below 0.2 · independent |
| Constraint at this position | ||
| Conservation | phyloP 5.9 | GERP 2.2, phastCons 1 |
| Regional constraint | o/e 0.92 | unconstrained · MANE · 10 kb · p 0.0024 · regional, not allelic |
| Overall | ||
| CADD | 24.5 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.
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
- CELSR3
- Protein
- p.Arg2886Pro
- Coding
- c.8657G>C
- MANE Select
- NM_001407
- Type
- single nucleotide variant
- Location
- chr3:48642366 (GRCh38)
- Gene constraint
- LOEUF 0.344 · pLI 1.00 (gnomAD)
Similar variants
- CELSR3 p.Arg2886= Likely benign ★★ same residue
- CELSR3 p.Ala2862Val Uncertain significance ★★ ⚠ same type
- CELSR3 p.Arg2345His Uncertain significance ★★ ⚠ same type
- CELSR3 p.Gly2265Ser Uncertain significance ★★ ⚠ same type
- CELSR3 p.Phe282Ser Uncertain significance ★★ ⚠ same type
- CELSR3 p.Val1107Met Uncertain significance ★★ same type
- CELSR3 p.Arg3189Gln Benign/Likely benign ★★ same type
- CELSR3 p.Arg3201Gln 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/celsr3-p-arg2886pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown