CEP164 p.Arg786=
c.2358G>A · rs2136351691 · VCV1086995
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
nephronophthisis 15
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 0.099 | GERP -1.5 |
| Overall | ||
| CADD | 2.516 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CEP164
- Protein
- p.Arg786=
- Coding
- c.2358G>A
- MANE Select
- NM_014956
- dbSNP
- rs2136351691
- Type
- single nucleotide variant
- Location
- chr11:117392300 (GRCh38)
- Gene constraint
- LOEUF 1.009 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.08 · 4 PDB
Disease context
nephronophthisis 15 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Senior-Loken syndrome (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adolescent, Adult, Childhood, Infancy
- Prevalence
- 1-9 / 1 000 000 (Worldwide)
Similar variants
- CEP164 p.Arg786Gln Uncertain significance ★★ ⚠ same residue
- CEP164 p.Arg786Trp Uncertain significance ★★ ⚠ same residue
- CEP164 c.1234-2A>T Likely pathogenic ★★ same condition
- CEP164 c.1724+1G>A Likely pathogenic ★★ same condition
- CEP164 c.1934+1G>A Likely pathogenic ★★ same condition
- CEP164 c.2361+1G>A Likely pathogenic ★★ same condition
- CEP164 c.2493+1G>A Likely pathogenic ★★ same condition
- CEP164 c.2914-1G>C 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/cep164-p-arg786 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown