CTCF p.Glu478=
c.1434G>A · rs2543484647 · VCV1772584
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00115%, 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 | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.6 | GERP -0.32, phastCons 1 |
| Overall | ||
| CADD | 8.142 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00115%
South Asian · 1/86,964 alleles
Overall
7e-05%
1/1,427,936 alleles · very rare
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.Glu478=
- Coding
- c.1434G>A
- MANE Select
- NM_006565
- dbSNP
- rs2543484647
- Type
- single nucleotide variant
- Location
- chr16:67626631 (GRCh38)
- Gene constraint
- LOEUF 0.205 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 59.45 · 21 PDB
- Residue 478
- a UniProt-annotated variant site (found in an endometrial carcinoma sample; uncertain significance); a β-strand
Similar variants
- CTCF p.Glu478Lys 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-glu478 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown