CEP164 p.Arg650=
c.1950G>T · rs753951348 · VCV597460
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000169%, nfe)
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 3.9 | GERP 0.35, phastCons 1 |
| Overall | ||
| CADD | 6.486 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000169%
European (non-Finnish) · 2/1,180,004 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000137%
2/1,461,864 alleles · very rare
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
- CEP164
- Protein
- p.Arg650=
- Coding
- c.1950G>T
- MANE Select
- NM_014956
- dbSNP
- rs753951348
- Type
- single nucleotide variant
- Location
- chr11:117390792 (GRCh38)
- Gene constraint
- LOEUF 1.009 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.08 · 4 PDB
Similar variants
- CEP164 p.Arg650Gln Uncertain significance ★ ⚠ same residue
- CEP164 p.Arg650Trp Conflicting classifications of pathogenicity ★ ⚠ same residue
- CEP164 c.1234-2A>T Likely pathogenic ★★ same type
- CEP164 c.1724+1G>A Likely pathogenic ★★ same type
- CEP164 c.1934+1G>A Likely pathogenic ★★ same type
- CEP164 c.2361+1G>A Likely pathogenic ★★ same type
- CEP164 c.2493+1G>A Likely pathogenic ★★ same type
- CEP164 c.2914-1G>C Likely pathogenic ★★ 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/cep164-p-arg650 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown