CELSR2 p.Arg2015=
c.6045G>A · rs72703204 · VCV3037800
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.96%, nfe)
Conditions
1
CELSR2-related disorder
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 0.94 | GERP -2.7, phastCons 1 |
| Overall | ||
| CADD | 6.584 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.96%
European (non-Finnish) · 46,675/1,179,918 alleles
Filtering AF
3.93%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.91%
Overall
3.21%
51,860/1,614,034 alleles · low-frequency
exomes 48,625/1,461,774 · genomes 3,235/152,260 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 3.96% | 25 |
| Remaining individualsnot grpmax-eligible | 2.74% | 36 |
| Admixed American | 1.64% | 61 |
| Finnishnot grpmax-eligible | 1.58% | 63 |
| Ashkenazi Jewishnot grpmax-eligible | 1.21% | 83 |
| South Asian | 0.686% | 146 |
| African / African-American | 0.609% | 164 |
| Amishnot grpmax-eligible | 0.439% | 228 |
| Middle Eastern | 0.429% | 233 |
| East Asian | 0.0111% | 8,973 |
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.Arg2015=
- Coding
- c.6045G>A
- MANE Select
- NM_001408
- dbSNP
- rs72703204
- Type
- single nucleotide variant
- Location
- chr1:109267579 (GRCh38)
- Gene constraint
- LOEUF 0.396 · pLI 1.00 (gnomAD)
Disease context
CELSR2-related disorder
Similar variants
- CELSR2 p.Arg2015Lys Benign ★ same residue
- CELSR2 p.Arg426Ter Uncertain significance same condition
- CELSR2 p.Arg881Ter Uncertain significance same condition
- CELSR2 p.Ala2579= Likely benign same condition
- CELSR2 p.Arg2191His Likely benign same condition
- CELSR2 p.Asn1182= Likely benign same condition
- CELSR2 p.Asn1830= Likely benign same condition
- CELSR2 p.Gln2053= Likely benign same condition
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-arg2015 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown