CEP295 p.Thr2600=
c.7800A>G · VCV4681489
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.288%, mid)
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 | GERP -1.8, phastCons 0.035 |
| Overall | ||
| CADD | 5.658 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.288%
Middle Eastern · 16/5,554 alleles
Filtering AF
0.181%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.147%
Overall
0.00433%
67/1,547,824 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.288% | 347 |
| South Asian | 0.0238% | 4,199 |
| Admixed American | 0.00393% | 25,471 |
| Remaining individualsnot grpmax-eligible | 0.00334% | 29,952 |
| European (non-Finnish) | 0.00236% | 42,379 |
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.Thr2600=
- Coding
- c.7800A>G
- MANE Select
- NM_033395
- Type
- single nucleotide variant
- Location
- chr11:93730263 (GRCh38)
- Gene constraint
- LOEUF 0.735 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 44.76
- Residue 2600
- a UniProt-annotated variant site (in sckl11; likely pathogenic); the 'alms motif' region
Similar variants
- 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
- CEP295 p.Glu179Lys 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-thr2600 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown