CEP250 p.Gln1079=
c.3237A>G · rs61733772 · VCV1165421
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0907%, nfe)
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 -0.37 | GERP -3.9, phastCons 0.001 |
| Overall | ||
| CADD | 3.325 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0907%
European (non-Finnish) · 1,070/1,180,010 alleles
Filtering AF
0.0861%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0843%
Overall
0.0716%
1,155/1,614,154 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0907% | 1,103 |
| Remaining individualsnot grpmax-eligible | 0.072% | 1,389 |
| Admixed American | 0.035% | 2,858 |
| African / African-American | 0.0173% | 5,773 |
| Finnishnot grpmax-eligible | 0.00937% | 10,673 |
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
- CEP250
- Protein
- p.Gln1079=
- Coding
- c.3237A>G
- MANE Select
- NM_007186
- dbSNP
- rs61733772
- Type
- single nucleotide variant
- Location
- chr20:35496646 (GRCh38)
- Gene constraint
- LOEUF 0.86 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.68 · 1 PDB
- Residue 1079
- a UniProt-annotated variant site (in crdhl2); a UniProt-annotated variant site (in crdhl2; also found in a family with non-syndromic retinitis pigmentosa)
Similar variants
- CEP250 p.Arg1045Ter Pathogenic/Likely pathogenic ★★ same type
- CEP250 p.Arg1155Ter Pathogenic/Likely pathogenic ★★ same type
- CEP250 p.Arg1336Ter Pathogenic/Likely pathogenic ★★ same type
- CEP250 p.Arg1343Ter Pathogenic/Likely pathogenic ★★ same type
- CEP250 p.Arg1499Ter Pathogenic/Likely pathogenic ★★ same type
- CEP250 p.Arg1695Ter Pathogenic/Likely pathogenic ★★ same type
- CEP250 p.Arg1869Ter Pathogenic/Likely pathogenic ★★ same type
- CEP250 p.Arg188Ter Pathogenic ★★ 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/cep250-p-gln1079 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown