CELSR3 p.His3294=
c.9882C>T · rs373106405 · VCV514123
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0546%, afr)
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 0.34 | GERP -4.1, phastCons 0.95 |
| Overall | ||
| CADD | 0.41 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0546%
African / African-American · 41/75,064 alleles
Filtering AF
0.0413%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0367%
Overall
0.00285%
46/1,613,670 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0546% | 1,831 |
| Admixed American | 0.00833% | 12,006 |
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.His3294=
- Coding
- c.9882C>T
- MANE Select
- NM_001407
- dbSNP
- rs373106405
- Type
- single nucleotide variant
- Location
- chr3:48639703 (GRCh38)
- Gene constraint
- LOEUF 0.344 · pLI 1.00 (gnomAD)
- Residue 3294
- the 'disordered' region
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-his3294 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown