CTCF p.Glu719=
c.2157G>A · rs778243342 · VCV742160
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.141%, sas)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 6.7 | GERP 2, phastCons 1 |
| Overall | ||
| CADD | 7.297 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.141%
South Asian · 128/90,988 alleles
Filtering AF
0.121%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.113%
Overall
0.00912%
147/1,612,276 alleles · rare
exomes 143/1,459,918 · genomes 4/152,358 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.141% | 711 |
| Middle Eastern | 0.0866% | 1,154 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,927 |
| European (non-Finnish) | 0.000509% | 196,651 |
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.Glu719=
- Coding
- c.2157G>A
- MANE Select
- NM_006565
- dbSNP
- rs778243342
- Type
- single nucleotide variant
- Location
- chr16:67637845 (GRCh38)
- Gene constraint
- LOEUF 0.205 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 59.45 · 21 PDB
- Residue 719
- a UniProt-annotated variant site (found in an endometrial carcinoma sample; uncertain significance)
Similar variants
- CTCF p.Glu719Val Uncertain significance ★ ⚠ same residue
- CTCF c.782-1G>C Pathogenic/Likely pathogenic ★★ same condition
- CTCF p.Arg368Cys Pathogenic ★★ same condition
- CTCF p.Pro378Leu Pathogenic/Likely pathogenic ★★ same condition
- CTCF p.Arg277Gln Uncertain significance ★★ ⚠ same condition
- CTCF p.Cys299Arg Uncertain significance ★★ ⚠ same condition
- CTCF p.Gly597Arg Uncertain significance ★★ ⚠ same condition
- CTCF p.Gly657Arg Uncertain significance ★★ ⚠ same condition
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-glu719 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown