CEP152 p.Arg673=
c.2019G>A · rs587783418 · VCV158239
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0267%, amr)
Conditions
2
Inborn genetic diseases
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 0.85 | GERP 4.5, phastCons 1 |
| Overall | ||
| CADD | 9.356 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0267%
Admixed American · 16/60,002 alleles
Filtering AF
0.0166%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0136%
Overall
0.00105%
17/1,613,958 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0267% | 3,750 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,486 |
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
- CEP152
- Protein
- p.Arg673=
- Coding
- c.2019G>A
- MANE Select
- NM_001194998
- dbSNP
- rs587783418
- Type
- single nucleotide variant
- Location
- chr15:48767463 (GRCh38)
- Gene constraint
- LOEUF 0.784 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.54 · 3 PDB
Similar variants
- CEP152 c.1908+1G>T Likely pathogenic ★★ same condition
- CEP152 c.540+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CEP152 c.972+2T>A Likely pathogenic ★★ same condition
- CEP152 p.Arg115Ter Pathogenic/Likely pathogenic ★★ same condition
- CEP152 p.Arg1309Ter Pathogenic/Likely pathogenic ★★ same condition
- CEP152 p.Arg267Ter Pathogenic/Likely pathogenic ★★ same condition
- CEP152 p.Arg987Ter Pathogenic/Likely pathogenic ★★ same condition
- CEP152 p.Gln265Pro Pathogenic/Likely pathogenic ★★ 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/cep152-p-arg673 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown