CELSR2 p.Pro1836=
c.5508G>A · rs368138606 · VCV3040958
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0493%, 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 |
|---|---|---|
| Pangolin | Δ0.20 | loss · gain 0.01 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP -7.6 | GERP -3.9 |
| Overall | ||
| CADD | 0.056 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0493%
Middle Eastern · 3/6,084 alleles
Filtering AF
0.0134%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00715%
Overall
0.00861%
139/1,614,070 alleles · ultra-rare
exomes 128/1,461,884 · genomes 11/152,186 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0493% | 2,028 |
| Admixed American | 0.0133% | 7,501 |
| African / African-American | 0.0107% | 9,363 |
| South Asian | 0.00988% | 10,122 |
| European (non-Finnish) | 0.00881% | 11,347 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,497 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
| East Asian | 0.00223% | 44,902 |
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.Pro1836=
- Coding
- c.5508G>A
- MANE Select
- NM_001408
- dbSNP
- rs368138606
- Type
- single nucleotide variant
- Location
- chr1:109264911 (GRCh38)
- Gene constraint
- LOEUF 0.396 · pLI 1.00 (gnomAD)
- Residue 1836
- the egf-like 6; calcium-binding domain
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-pro1836 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown