CTCF p.Tyr502=
c.1506C>T · VCV4930459
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0298%, 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 -9.9 | GERP -3.8 |
| Overall | ||
| CADD | 2.352 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0298%
Admixed American · 12/40,210 alleles
Filtering AF
0.0171%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0135%
Overall
0.00185%
27/1,459,594 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0298% | 3,351 |
| East Asian | 0.00988% | 10,118 |
| Remaining individualsnot grpmax-eligible | 0.00913% | 10,953 |
| South Asian | 0.00147% | 67,974 |
| European (non-Finnish) | 0.000456% | 219,435 |
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
- CTCF
- Protein
- p.Tyr502=
- Coding
- c.1506C>T
- MANE Select
- NM_006565
- Type
- single nucleotide variant
- Location
- chr16:67626703 (GRCh38)
- Gene constraint
- LOEUF 0.205 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 59.45 · 21 PDB
- Residue 502
- a UniProt-annotated variant site (found in an endometrial carcinoma sample; uncertain significance)
Similar variants
- CTCF p.Tyr502fs Likely pathogenic ★ same residue
- CTCF c.782-1G>A Pathogenic/Likely pathogenic ★★ same type
- CTCF c.782-1G>C Pathogenic/Likely pathogenic ★★ same type
- CTCF c.782-2A>G Pathogenic/Likely pathogenic ★★ same type
- CTCF c.782-2A>T Pathogenic ★★ same type
- CTCF p.Arg283His Likely pathogenic ★★ ⚠ same type
- CTCF p.Arg342Cys Pathogenic/Likely pathogenic ★★ same type
- CTCF p.Arg342His Pathogenic/Likely pathogenic ★★ 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/ctcf-p-tyr502 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown