CELSR3 p.Arg2886=
c.8658A>G · rs151064682 · VCV1176021
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0549%, nfe)
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 0.85 | GERP 1.3, phastCons 1 |
| Overall | ||
| CADD | 8.087 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0549%
European (non-Finnish) · 648/1,179,534 alleles
Filtering AF
0.0514%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.05%
Overall
0.0419%
675/1,612,330 alleles · ultra-rare
exomes 642/1,460,238 · genomes 33/152,092 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0549% | 1,820 |
| Remaining individualsnot grpmax-eligible | 0.024% | 4,163 |
| African / African-American | 0.00801% | 12,491 |
| South Asian | 0.00549% | 18,200 |
| Finnishnot grpmax-eligible | 0.00158% | 63,184 |
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
- CELSR3
- Protein
- p.Arg2886=
- Coding
- c.8658A>G
- MANE Select
- NM_001407
- dbSNP
- rs151064682
- Type
- single nucleotide variant
- Location
- chr3:48642365 (GRCh38)
- Gene constraint
- LOEUF 0.344 · pLI 1.00 (gnomAD)
Similar variants
- CELSR3 p.Arg2886Pro Uncertain significance ★ 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-arg2886 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown