CTCF p.Lys244=
c.732A>G · rs753101673 · VCV755205
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00441%, 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 3.5 | GERP -0.54, phastCons 1 |
| Overall | ||
| CADD | 8.351 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00441%
European (non-Finnish) · 52/1,180,048 alleles
Filtering AF
0.00342%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0031%
Overall
0.00335%
54/1,614,112 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00441% | 22,693 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,484 |
| African / African-American | 0.00133% | 74,954 |
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.Lys244=
- Coding
- c.732A>G
- MANE Select
- NM_006565
- dbSNP
- rs753101673
- Type
- single nucleotide variant
- Location
- chr16:67611564 (GRCh38)
- Gene constraint
- LOEUF 0.205 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 59.45 · 21 PDB
- Residue 244
- a UniProt-annotated variant site (found in an endometrial carcinoma sample; uncertain significance)
Similar variants
- 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
- CTCF p.Arg368Cys 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-lys244 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown