CCT2 p.Tyr439=
c.1317T>C · rs376042508 · VCV1091376
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0133%, amr)
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 -16 | GERP -4.6 |
| Overall | ||
| CADD | 0.256 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0133%
Admixed American · 8/59,960 alleles
Filtering AF
0.00662%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00483%
Overall
0.00236%
38/1,611,920 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0133% | 7,495 |
| African / African-American | 0.012% | 8,319 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,797 |
| European (non-Finnish) | 0.00153% | 65,457 |
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.Tyr439=
- Coding
- c.1317T>C
- MANE Select
- NM_006431
- dbSNP
- rs376042508
- Type
- single nucleotide variant
- Location
- chr12:69598053 (GRCh38)
- Gene constraint
- LOEUF 0.445 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 89.85 · 71 PDB
- Residue 439
- an α-helix
Similar variants
- CCT2 p.Tyr439His 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-tyr439 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown