CELSR1 p.Ser3009=
c.9027C>T · VCV4948337
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.9%, eas)
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 -6.1 | GERP -2.5 |
| Overall | ||
| CADD | 0.347 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.9%
East Asian · 849/44,628 alleles
Filtering AF
1.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.75%
Overall
0.0612%
983/1,605,652 alleles · low-frequency
exomes 914/1,453,344 · genomes 69/152,308 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.9% | 53 |
| Admixed American | 0.0442% | 2,265 |
| Remaining individualsnot grpmax-eligible | 0.0419% | 2,385 |
| South Asian | 0.00774% | 12,912 |
| European (non-Finnish) | 0.00629% | 15,904 |
| African / African-American | 0.00134% | 74,662 |
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.Ser3009=
- Coding
- c.9027C>T
- MANE Select
- NM_001378328
- Type
- single nucleotide variant
- Location
- chr22:46364004 (GRCh38)
- Gene constraint
- LOEUF 0.564 · pLI <0.01 (gnomAD)
- Residue 3009
- a UniProt-annotated variant site (in lmphm9); 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-ser3009 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown