CELSR1 p.Pro2301=
c.6903G>A · rs137999772 · VCV3025584
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.569%, afr)
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 -13 | GERP -2.7 |
| Overall | ||
| CADD | 0.225 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.569%
African / African-American · 417/73,250 alleles
Filtering AF
0.524%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.506%
Overall
0.0329%
508/1,546,408 alleles · rare
exomes 254/1,394,072 · genomes 254/152,336 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.569% | 176 |
| Middle Eastern | 0.135% | 743 |
| Remaining individualsnot grpmax-eligible | 0.0484% | 2,065 |
| Admixed American | 0.023% | 4,341 |
| South Asian | 0.00832% | 12,019 |
| Finnishnot grpmax-eligible | 0.00365% | 27,384 |
| European (non-Finnish) | 0.00279% | 35,803 |
| East Asian | 0.00242% | 41,292 |
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
- CELSR1
- Protein
- p.Pro2301=
- Coding
- c.6903G>A
- MANE Select
- NM_001378328
- dbSNP
- rs137999772
- Type
- single nucleotide variant
- Location
- chr22:46382031 (GRCh38)
- Gene constraint
- LOEUF 0.564 · pLI <0.01 (gnomAD)
- Residue 2301
- a UniProt-annotated variant site (in lmphm9); the gain-b domain; the 'disordered' region
Similar variants
- CELSR1 p.Ala2442Val Uncertain significance ★★ ⚠ same type
- CELSR1 p.Ala2955Thr Uncertain significance ★★ ⚠ same type
- CELSR1 p.Ala396Ser Uncertain significance ★★ ⚠ same type
- CELSR1 p.Ala617Ser Uncertain significance ★★ ⚠ same type
- CELSR1 p.Arg1323Gln Uncertain significance ★★ ⚠ same type
- CELSR1 p.Arg1379His Uncertain significance ★★ ⚠ same type
- CELSR1 p.Arg1643Gln Uncertain significance ★★ ⚠ same type
- CELSR1 p.Arg1720Trp Uncertain significance ★★ ⚠ 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/celsr1-p-pro2301 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown