CCT2 p.Ile33=
c.99C>T · rs780733349 · VCV1114014
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00542%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.20 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.6 | GERP -4.1 |
| Overall | ||
| CADD | 12.15 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00542%
African / African-American · 4/73,794 alleles
Filtering AF
0.00176%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00105%
Overall
0.00106%
17/1,599,808 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00542% | 18,449 |
| Admixed American | 0.00174% | 57,346 |
| Remaining individualsnot grpmax-eligible | 0.00162% | 61,868 |
| South Asian | 0.00114% | 87,676 |
| European (non-Finnish) | 0.000851% | 117,477 |
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
- CCT2
- Protein
- p.Ile33=
- Coding
- c.99C>T
- MANE Select
- NM_006431
- dbSNP
- rs780733349
- Type
- single nucleotide variant
- Location
- chr12:69586773 (GRCh38)
- Gene constraint
- LOEUF 0.445 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 89.85 · 71 PDB
- Residue 33
- an α-helix
Similar variants
- CCT2 p.Ile33Val Uncertain significance ★ ⚠ same residue
- CCT2 p.Ala128Thr Uncertain significance ★★ ⚠ same type
- CCT2 p.Ala133Val Uncertain significance ★★ ⚠ same type
- CCT2 p.Ala145Val Uncertain significance ★★ ⚠ same type
- CCT2 p.Arg156Cys Uncertain significance ★★ ⚠ same type
- CCT2 p.Arg255Gln Uncertain significance ★★ same type
- CCT2 p.Arg255Trp Uncertain significance ★★ ⚠ same type
- CCT2 p.Arg281Cys Uncertain significance ★★ ⚠ 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/cct2-p-ile33 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown