CEP295 p.Arg694=
c.2082C>T · VCV4681452
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0773%, sas)
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 -1.5 | GERP -3 |
| Overall | ||
| CADD | 2.254 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0773%
South Asian · 65/84,040 alleles
Filtering AF
0.0622%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0567%
Overall
0.0121%
188/1,551,414 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0773% | 1,293 |
| Finnishnot grpmax-eligible | 0.0368% | 2,719 |
| Remaining individualsnot grpmax-eligible | 0.0116% | 8,589 |
| European (non-Finnish) | 0.00785% | 12,742 |
| East Asian | 0.00733% | 13,635 |
| African / African-American | 0.00137% | 73,164 |
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
- CEP295
- Protein
- p.Arg694=
- Coding
- c.2082C>T
- MANE Select
- NM_033395
- Type
- single nucleotide variant
- Location
- chr11:93696994 (GRCh38)
- Gene constraint
- LOEUF 0.735 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 44.76
- Residue 694
- a UniProt-annotated variant site (in sckl11; likely pathogenic)
Similar variants
- CEP295 p.Arg694Ser Uncertain significance ★ ⚠ same residue
- CEP295 p.Gln2146His Uncertain significance ★★ ⚠ same type
- CEP295 p.Gln998Arg Uncertain significance ★★ ⚠ same type
- CEP295 p.Thr451Arg Uncertain significance ★★ ⚠ same type
- CEP295 p.Gln1506= Benign ★★ same type
- CEP295 p.Gln1728= Benign ★★ same type
- CEP295 p.Gln80Lys Benign ★★ same type
- CEP295 p.Glu1026Lys Benign ★★ ⚠ 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/cep295-p-arg694 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown