CCT2 p.Thr261=
c.783A>G · rs1043434 · VCV1164723
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 31.9%, mid) — too common for a highly-penetrant pathogenic allele
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 2.4 | GERP 1, phastCons 1 |
| Overall | ||
| CADD | 9.117 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
31.9%
Middle Eastern · 1,930/6,052 alleles
Filtering AF
30.7%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 30.2%
Overall
21.9%
353,822/1,612,476 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 31.9% | 3 |
| South Asian | 27.9% | 4 |
| East Asian | 25.1% | 4 |
| Ashkenazi Jewishnot grpmax-eligible | 24.8% | 4 |
| Remaining individualsnot grpmax-eligible | 22.6% | 4 |
| European (non-Finnish) | 22.2% | 5 |
| Finnishnot grpmax-eligible | 20.8% | 5 |
| Amishnot grpmax-eligible | 20.4% | 5 |
| Admixed American | 18.4% | 5 |
| African / African-American | 10.8% | 9 |
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.Thr261=
- Coding
- c.783A>G
- MANE Select
- NM_006431
- dbSNP
- rs1043434
- Type
- single nucleotide variant
- Location
- chr12:69593008 (GRCh38)
- Gene constraint
- LOEUF 0.445 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 89.85 · 71 PDB
- Residue 261
- a modified residue (phosphothreonine); an α-helix
Similar variants
- 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
- CCT2 p.Arg281His 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-thr261 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown