CEP68 p.Pro486=
c.1458C>T · VCV4831911
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0495%, mid)
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 -1.3 | GERP -4 |
| Overall | ||
| CADD | 3.636 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0495%
Middle Eastern · 3/6,062 alleles
Filtering AF
0.0134%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00718%
Overall
0.00551%
89/1,614,080 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0495% | 2,021 |
| European (non-Finnish) | 0.00653% | 15,325 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,835 |
| Admixed American | 0.00333% | 30,006 |
| South Asian | 0.0022% | 45,536 |
| Finnishnot grpmax-eligible | 0.00156% | 63,996 |
| African / African-American | 0.00133% | 75,040 |
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
- CEP68
- Protein
- p.Pro486=
- Coding
- c.1458C>T
- MANE Select
- NM_015147
- Type
- single nucleotide variant
- Location
- chr2:65072554 (GRCh38)
- Gene constraint
- LOEUF 0.627 · pLI 0.05 (gnomAD)
- Structure
- AlphaFold pLDDT 49.36
Similar variants
- CEP68 c.2007+9C>G Benign ★★ same type
- CEP68 p.Arg217His Benign ★★ ⚠ same type
- CEP68 p.His566= Benign/Likely benign ★★ same type
- CEP68 p.Phe367Tyr Benign ★★ same type
- CEP68 p.Ser447= Benign ★★ same type
- CEP68 p.Val607Ala Benign ★★ same type
- CEP68 p.Ala163Thr Uncertain significance ★ ⚠ same type
- CEP68 p.Ala214Val 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/cep68-p-pro486 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown