CCT2 p.Phe12=
c.36T>C · rs111309939 · VCV1167582
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.212%, 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 1.8 | GERP 0.18, phastCons 1 |
| Overall | ||
| CADD | 14.42 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.212%
European (non-Finnish) · 2,505/1,179,616 alleles
Filtering AF
0.205%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.203%
Overall
0.18%
2,904/1,613,736 alleles · rare
exomes 2,720/1,461,424 · genomes 184/152,312 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.212% | 471 |
| South Asian | 0.21% | 477 |
| Remaining individualsnot grpmax-eligible | 0.142% | 702 |
| Finnishnot grpmax-eligible | 0.0875% | 1,143 |
| Middle Eastern | 0.066% | 1,516 |
| Admixed American | 0.06% | 1,667 |
| African / African-American | 0.0293% | 3,411 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
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.Phe12=
- Coding
- c.36T>C
- MANE Select
- NM_006431
- dbSNP
- rs111309939
- Type
- single nucleotide variant
- Location
- chr12:69586302 (GRCh38)
- Gene constraint
- LOEUF 0.445 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 89.85 · 71 PDB
Similar variants
- CCT2 p.Phe12Leu 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-phe12 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown