CTCF p.Lys496Ter
c.1485dup · rs2543484844 · VCV2446041
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Rare
ultra-rare (gnomAD MAF 1.909e-06)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 8 of 12 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 3.2 | GERP 0.95, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
dbSNP / gnomAD
Global frequency
0.000191%
via dbSNP · ultra-rare
No ancestry breakdown or filtering allele frequency is available for this variant, so BA1/BS1 cannot be assessed from this figure alone.
Variant & gene context
- Gene
- CTCF
- Protein
- p.Lys496Ter
- Coding
- c.1485dup
- MANE Select
- NM_006565
- dbSNP
- rs2543484844
- Type
- Duplication
- Location
- chr16:67626679 (GRCh38)
- Gene constraint
- LOEUF 0.205 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 59.45 · 21 PDB
- Residue 496
- a UniProt-annotated variant site (found in an endometrial carcinoma sample; uncertain significance)
Similar variants
- CTCF p.Thr204fs Pathogenic ★★ same type
- CTCF p.Ala148fs Likely pathogenic ★ same type
- CTCF p.Arg396fs Pathogenic ★ same type
- CTCF p.Arg596fs Pathogenic ★ same type
- CTCF p.Asp290fs Likely pathogenic ★ same type
- CTCF p.Cys353fs Likely pathogenic ★ same type
- CTCF p.Gln106fs Pathogenic ★ same type
- CTCF p.Gly111fs 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-lys496ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown