CEP97 p.Leu230=
c.690C>G · rs144895544 · VCV2084415
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.61%, sas)
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 1.8 | GERP 0.82, phastCons 1 |
| Overall | ||
| CADD | 9.689 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.61%
South Asian · 1,464/91,056 alleles
Filtering AF
1.54%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.51%
Overall
0.0963%
1,554/1,614,008 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.61% | 62 |
| Remaining individualsnot grpmax-eligible | 0.109% | 919 |
| Middle Eastern | 0.0825% | 1,212 |
| Admixed American | 0.00833% | 11,999 |
| African / African-American | 0.008% | 12,506 |
| East Asian | 0.00446% | 22,442 |
| European (non-Finnish) | 0.000339% | 294,984 |
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.Leu230=
- Coding
- c.690C>G
- MANE Select
- NM_024548
- dbSNP
- rs144895544
- Type
- single nucleotide variant
- Location
- chr3:101732616 (GRCh38)
- Gene constraint
- LOEUF 0.847 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 58.89
- Residue 230
- the lrrct domain
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-leu230 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown