CELSR2 p.Phe2566=
c.7698C>T · rs367633301 · VCV3048721
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0991%, mid)
Conditions
1
CELSR2-related disorder
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 -6.7 | GERP -3.4 |
| Overall | ||
| CADD | 3.582 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0991%
Middle Eastern · 6/6,056 alleles
Filtering AF
0.043%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0295%
Overall
0.00285%
46/1,613,094 alleles · ultra-rare
exomes 43/1,461,626 · genomes 3/151,468 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0991% | 1,009 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,926 |
| European (non-Finnish) | 0.00263% | 38,059 |
| Admixed American | 0.00167% | 59,964 |
| Finnishnot grpmax-eligible | 0.00157% | 63,740 |
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.Phe2566=
- Coding
- c.7698C>T
- MANE Select
- NM_001408
- dbSNP
- rs367633301
- Type
- single nucleotide variant
- Location
- chr1:109271407 (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.Asn1182= Likely benign same condition
- CELSR2 p.Asn1830= Likely benign same condition
- CELSR2 p.Gln2053= 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-phe2566 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown