CTCF p.Lys211fs
c.633del · VCV4081928
Pathogenic
No assertion criteria
Classification
Pathogenic
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
CTCF-related neurodevelopmental disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 3 of 12 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 1.4 | GERP -0.74, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CTCF
- Protein
- p.Lys211fs
- Coding
- c.633del
- MANE Select
- NM_006565
- Type
- Deletion
- Location
- chr16:67611463 (GRCh38)
- Gene constraint
- LOEUF 0.205 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 59.45 · 21 PDB
- Residue 211
- 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.Lys206fs Pathogenic ★★ same condition
- CTCF p.Lys258fs Pathogenic ★★ same condition
- CTCF p.Asn241fs Likely pathogenic ★ same condition
- CTCF p.Glu230fs Pathogenic ★ same condition
- CTCF p.Leu98fs Pathogenic ★ same condition
- CTCF p.Pro119fs Likely pathogenic ★ same condition
- CTCF p.Val100fs Likely pathogenic ★ same condition
- CTCF p.Tyr545fs 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-lys211fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown