CELSR3 p.Gly3053=
c.9159C>T · rs372683231 · VCV753908
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0983%, amr)
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 -4.5 | GERP -3.6 |
| Overall | ||
| CADD | 0.087 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0983%
Admixed American · 59/60,022 alleles
Filtering AF
0.0782%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0709%
Overall
0.0105%
169/1,612,624 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0983% | 1,017 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,248 |
| European (non-Finnish) | 0.00822% | 12,164 |
| African / African-American | 0.004% | 25,005 |
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.Gly3053=
- Coding
- c.9159C>T
- MANE Select
- NM_001407
- dbSNP
- rs372683231
- Type
- single nucleotide variant
- Location
- chr3:48640426 (GRCh38)
- Gene constraint
- LOEUF 0.344 · pLI 1.00 (gnomAD)
Similar variants
- 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
- CELSR3 p.Arg3201Gln 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-gly3053 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown