CELSR3 p.Gly2824=
c.8472C>T · rs61729238 · VCV783380
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 5.95%, afr) — too common for a highly-penetrant pathogenic allele
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 -7.1 | GERP -4.5 |
| Overall | ||
| CADD | 0.103 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.95%
African / African-American · 4,463/75,028 alleles
Filtering AF
5.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.74%
Overall
0.334%
5,394/1,613,110 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 5.95% | 17 |
| Middle Eastern | 0.546% | 183 |
| Remaining individualsnot grpmax-eligible | 0.487% | 206 |
| Admixed American | 0.417% | 240 |
| Finnishnot grpmax-eligible | 0.0412% | 2,427 |
| South Asian | 0.0384% | 2,602 |
| European (non-Finnish) | 0.0234% | 4,275 |
| East Asian | 0.0156% | 6,411 |
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.Gly2824=
- Coding
- c.8472C>T
- MANE Select
- NM_001407
- dbSNP
- rs61729238
- Type
- single nucleotide variant
- Location
- chr3:48642819 (GRCh38)
- Gene constraint
- LOEUF 0.344 · pLI 1.00 (gnomAD)
Similar variants
- CELSR3 p.Gly2824Ala 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.Arg2886= Likely benign ★★ same type
- CELSR3 p.Arg3189Gln Benign/Likely 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-gly2824 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown