CELSR2 p.Asn1182=
c.3546C>T · rs183828529 · VCV3033110
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0805%, eas)
Conditions
1
CELSR2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.87 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.4 | GERP -1.3 |
| Overall | ||
| CADD | 8.414 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0805%
East Asian · 33/40,990 alleles
Filtering AF
0.0589%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0515%
Overall
0.00336%
52/1,548,704 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0805% | 1,242 |
| Admixed American | 0.00786% | 12,719 |
| African / African-American | 0.00684% | 14,628 |
| Remaining individualsnot grpmax-eligible | 0.00167% | 60,008 |
| South Asian | 0.00119% | 84,292 |
| European (non-Finnish) | 0.000698% | 143,183 |
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
- CELSR2
- Protein
- p.Asn1182=
- Coding
- c.3546C>T
- MANE Select
- NM_001408
- dbSNP
- rs183828529
- Type
- single nucleotide variant
- Location
- chr1:109258667 (GRCh38)
- Gene constraint
- LOEUF 0.396 · pLI 1.00 (gnomAD)
Disease context
CELSR2-related disorder
Similar variants
- CELSR2 p.Arg426Ter Uncertain significance same condition
- CELSR2 p.Arg881Ter Uncertain significance same condition
- CELSR2 p.Ala2579= Likely benign same condition
- CELSR2 p.Arg2015= Benign same condition
- CELSR2 p.Arg2191His Likely benign same condition
- CELSR2 p.Asn1830= Likely benign same condition
- CELSR2 p.Gln2053= Likely benign same condition
- CELSR2 p.Ile2250= Likely benign same condition
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/celsr2-p-asn1182 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown