CTCF c.*4C>T
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0155%, sas)
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 -0.35 | GERP -4.1 |
| Non-coding constraint | Z 0.75 | 1 kb window · o/e 0.95 · regional · uncalibrated |
| Overall | ||
| CADD | 1.266 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0155%
South Asian · 14/90,454 alleles
Filtering AF
0.00936%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0075%
Overall
0.00144%
23/1,600,992 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0155% | 6,461 |
| East Asian | 0.00448% | 22,333 |
| Remaining individualsnot grpmax-eligible | 0.00324% | 30,871 |
| Finnishnot grpmax-eligible | 0.00157% | 63,850 |
| European (non-Finnish) | 0.000341% | 293,226 |
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
- Coding
- c.*4C>T
- MANE Select
- NM_006565
- dbSNP
- rs746166629
- Type
- single nucleotide variant
- Location
- chr16:67637876 (GRCh38)
- Gene constraint
- LOEUF 0.205 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 59.45 · 21 PDB
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-c-star-4c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown