CEP97 p.Arg608=
c.1824A>G · rs145813958 · VCV2071886
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0384%, 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 4.7 | GERP 1.5, phastCons 1 |
| Overall | ||
| CADD | 11.52 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0384%
European (non-Finnish) · 451/1,174,328 alleles
Filtering AF
0.0354%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0343%
Overall
0.0289%
464/1,604,784 alleles · ultra-rare
exomes 443/1,452,568 · genomes 21/152,216 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0384% | 2,604 |
| Remaining individualsnot grpmax-eligible | 0.0129% | 7,768 |
| Admixed American | 0.00509% | 19,647 |
| African / African-American | 0.00268% | 37,258 |
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.Arg608=
- Coding
- c.1824A>G
- MANE Select
- NM_024548
- dbSNP
- rs145813958
- Type
- single nucleotide variant
- Location
- chr3:101762491 (GRCh38)
- Gene constraint
- LOEUF 0.847 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 58.89
- Residue 608
- the 'ccp110-binding' region; the 'interaction with mphosph9' region
Similar variants
- 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
- CEP97 p.Arg615Cys 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-arg608 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown