CTCF p.Asn713Lys
c.2139C>A · rs146712579 · VCV983075
Computational evidence
| Protein change | ||
| AlphaMissense | 0.4895 | ambiguous |
|---|---|---|
| REVEL | 0.145 | moderately benign-leaning |
| SaProt | LLR -6.51 | tolerated |
| ⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -9.6 | GERP -4.1 |
| Regional constraint | o/e 0.20 | constrained · MANE · 43 bp · p 8.2e-05 · regional, not allelic |
| Overall | ||
| CADD | 9.344 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
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.Asn713Lys
- Coding
- c.2139C>A
- MANE Select
- NM_006565
- dbSNP
- rs146712579
- Type
- single nucleotide variant
- Location
- chr16:67637827 (GRCh38)
- Gene constraint
- LOEUF 0.205 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 59.45 · 21 PDB
- Residue 713
- the 'disordered' region; a UniProt-annotated variant site (found in an endometrial carcinoma sample; uncertain significance)
Disease context
CTCF-related neurodevelopmental disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor CTCF-related neurodevelopmental disorder (Orphanet):
- Inheritance
- Autosomal dominant
- Onset
- Antenatal, Childhood, Infancy, Neonatal
Similar variants
- CTCF p.Asn713= Benign/Likely benign ★★ same residue
- CTCF c.782-1G>A Pathogenic/Likely pathogenic ★★ same condition
- CTCF c.782-1G>C Pathogenic/Likely pathogenic ★★ same condition
- CTCF c.782-2A>G Pathogenic/Likely pathogenic ★★ same condition
- CTCF c.782-2A>T Pathogenic ★★ same condition
- CTCF p.Arg283His Likely pathogenic ★★ same condition
- CTCF p.Arg342Cys Pathogenic/Likely pathogenic ★★ same condition
- CTCF p.Arg342His Pathogenic/Likely pathogenic ★★ 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-asn713lys (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown