CEP97 p.Ile223=
c.669C>T · rs193228690 · VCV2046500
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0426%, 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 -7.3 | GERP -3.4 |
| Overall | ||
| CADD | 4.488 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0426%
African / African-American · 32/75,052 alleles
Filtering AF
0.031%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0271%
Overall
0.00322%
52/1,614,044 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0426% | 2,345 |
| Admixed American | 0.0117% | 8,574 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,624 |
| European (non-Finnish) | 0.000763% | 131,101 |
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
- CEP97
- Protein
- p.Ile223=
- Coding
- c.669C>T
- MANE Select
- NM_024548
- dbSNP
- rs193228690
- Type
- single nucleotide variant
- Location
- chr3:101732595 (GRCh38)
- Gene constraint
- LOEUF 0.847 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 58.89
- Residue 223
- the lrrct domain
Similar variants
- CEP97 p.Ile223Val Uncertain significance ★ ⚠ same residue
- CEP97 p.Ala164Thr Uncertain significance ★★ ⚠ same type
- CEP97 p.Ala624Gly Uncertain significance ★★ ⚠ same type
- CEP97 p.Arg259Gln Uncertain significance ★★ ⚠ same type
- CEP97 p.Arg468Ile Uncertain significance ★★ ⚠ same type
- CEP97 p.Arg570Gln Uncertain significance ★★ ⚠ same type
- CEP97 p.Arg585Cys Uncertain significance ★★ ⚠ same type
- CEP97 p.Arg591Cys 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/cep97-p-ile223 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown