CEP170B p.Pro298Leu
c.893C>T · rs201541467 · VCV3041289
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.65%, eas)
Conditions
1
CEP170B-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.013 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.18 | GERP -3.8 |
| Regional constraint | o/e 1.00 | unconstrained · MANE · 19 kb · p 0.99 · regional, not allelic |
| Overall | ||
| CADD | 8.767 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.65%
East Asian · 739/44,794 alleles
Filtering AF
1.55%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.51%
Overall
0.121%
1,942/1,610,864 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.65% | 61 |
| South Asian | 0.426% | 234 |
| Remaining individualsnot grpmax-eligible | 0.207% | 483 |
| European (non-Finnish) | 0.0554% | 1,806 |
| Admixed American | 0.0284% | 3,521 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0271% | 3,692 |
| Middle Eastern | 0.0165% | 6,058 |
| Finnishnot grpmax-eligible | 0.00642% | 15,586 |
| African / African-American | 0.00534% | 18,738 |
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
- CEP170B
- Protein
- p.Pro298Leu
- Coding
- c.893C>T
- MANE Select
- NM_001112726
- dbSNP
- rs201541467
- Type
- single nucleotide variant
- Location
- chr14:104883350 (GRCh38)
- Gene constraint
- LOEUF 0.682 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 47.31
- Residue 298
- the 'disordered' region
Disease context
CEP170B-related disorder
Similar variants
- CEP170B c.3879-7G>C Benign same condition
- CEP170B c.3879-8G>A Benign same condition
- CEP170B c.4271+8G>A Likely benign same condition
- CEP170B c.4365+7G>A Likely benign same condition
- CEP170B p.Ala1177= Likely benign same condition
- CEP170B p.Ala127= Likely benign same condition
- CEP170B p.Ala302Val Likely benign same condition
- CEP170B p.Ala369Val Likely benign same condition
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/cep170b-p-pro298leu (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown