CEP170 p.Ser450=
c.1350G>A · VCV4226017
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00439%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.05 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.2 | GERP 0.87, phastCons 1 |
| Overall | ||
| CADD | 13.97 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00439%
South Asian · 4/91,076 alleles
Filtering AF
0.00157%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00134%
Overall
0.00223%
36/1,613,630 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00439% | 22,769 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,602 |
| African / African-American | 0.00267% | 37,448 |
| European (non-Finnish) | 0.00229% | 43,693 |
| East Asian | 0.00223% | 44,896 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,440 |
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
- CEP170
- Protein
- p.Ser450=
- Coding
- c.1350G>A
- MANE Select
- NM_014812
- Type
- single nucleotide variant
- Location
- chr1:243185995 (GRCh38)
- Gene constraint
- LOEUF 0.261 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 46.25 · 1 PDB
Similar variants
- CEP170 p.Val1524Met Uncertain significance ★★ ⚠ same type
- CEP170 c.4319+9A>T Benign ★★ same type
- CEP170 p.Met1275Val Benign ★★ same type
- CEP170 p.Tyr1291= Benign/Likely benign ★★ same type
- CEP170 c.195+1G>A Uncertain significance ★ same type
- CEP170 p.Ala1163Val Uncertain significance ★ ⚠ same type
- CEP170 p.Ala1310Thr Uncertain significance ★ ⚠ same type
- CEP170 p.Ala1392Gly 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/cep170-p-ser450 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown