CTCF p.Arg603=
c.1809C>A · rs1328942523 · VCV1780521
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 -2 | GERP -3.8 |
| Overall | ||
| CADD | 3.063 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CTCF
- Protein
- p.Arg603=
- Coding
- c.1809C>A
- MANE Select
- NM_006565
- dbSNP
- rs1328942523
- Type
- single nucleotide variant
- Location
- chr16:67629505 (GRCh38)
- Gene constraint
- LOEUF 0.205 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 59.45 · 21 PDB
- Residue 603
- the 'disordered' region; a UniProt-annotated variant site (found in an endometrial carcinoma sample; uncertain significance)
Similar variants
- 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
- CTCF p.Ile511Val 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-arg603 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown