CELSR2 p.Ser2560=
c.7680G>A · rs141656858 · VCV2773280
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.265%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.93 | acceptor gain, 2 bp away · raw score · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.4 | GERP -3.4 |
| Overall | ||
| CADD | 16.87 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.265%
Middle Eastern · 16/6,046 alleles
Filtering AF
0.233%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.221%
Overall
0.0266%
429/1,612,466 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.265% | 378 |
| African / African-American | 0.263% | 380 |
| East Asian | 0.0604% | 1,656 |
| Admixed American | 0.0551% | 1,816 |
| Remaining individualsnot grpmax-eligible | 0.0464% | 2,155 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0237% | 4,228 |
| European (non-Finnish) | 0.00949% | 10,533 |
| South Asian | 0.00659% | 15,170 |
| Finnishnot grpmax-eligible | 0.00471% | 21,213 |
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.Ser2560=
- Coding
- c.7680G>A
- MANE Select
- NM_001408
- dbSNP
- rs141656858
- Type
- single nucleotide variant
- Location
- chr1:109271389 (GRCh38)
- Gene constraint
- LOEUF 0.396 · pLI 1.00 (gnomAD)
Similar variants
- CELSR2 p.Ser2560Leu Uncertain significance ★ ⚠ same residue
- CELSR2 c.8338+1G>C Uncertain significance ★★ same type
- CELSR2 p.Ala1114Val Uncertain significance ★★ ⚠ same type
- CELSR2 p.Ala2145Thr Uncertain significance ★★ ⚠ same type
- CELSR2 p.Ala2574Thr Uncertain significance ★★ ⚠ same type
- CELSR2 p.Arg1171Gln Uncertain significance ★★ ⚠ same type
- CELSR2 p.Arg1328His Uncertain significance ★★ ⚠ same type
- CELSR2 p.Arg1400His 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/celsr2-p-ser2560 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown