CTCF p.Val6=
c.18C>T · rs549711902 · VCV745878
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.28%, 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 0.19 | GERP -3, phastCons 0.99 |
| Overall | ||
| CADD | 7.707 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.28%
South Asian · 840/65,768 alleles
Filtering AF
1.21%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.18%
Overall
0.0636%
945/1,485,572 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.28% | 78 |
| Remaining individualsnot grpmax-eligible | 0.0825% | 1,212 |
| European (non-Finnish) | 0.00484% | 20,665 |
| Finnishnot grpmax-eligible | 0.00336% | 29,750 |
| African / African-American | 0.0028% | 35,721 |
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.Val6=
- Coding
- c.18C>T
- MANE Select
- NM_006565
- dbSNP
- rs549711902
- Type
- single nucleotide variant
- Location
- chr16:67610850 (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-p-val6 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown