CTCF p.Lys323=
c.969G>A · rs777402247 · VCV740205
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0944%, sas)
Conditions
1
Inborn genetic diseases
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 9.8 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 13.17 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0944%
South Asian · 86/91,078 alleles
Filtering AF
0.0782%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0723%
Overall
0.00843%
136/1,614,124 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0944% | 1,059 |
| East Asian | 0.0646% | 1,548 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,682 |
| European (non-Finnish) | 0.000847% | 118,001 |
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.Lys323=
- Coding
- c.969G>A
- MANE Select
- NM_006565
- dbSNP
- rs777402247
- Type
- single nucleotide variant
- Location
- chr16:67616761 (GRCh38)
- Gene constraint
- LOEUF 0.205 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 59.45 · 21 PDB
- Residue 323
- a UniProt-annotated variant site (found in an endometrial carcinoma sample; uncertain significance)
Similar variants
- CTCF c.782-1G>C Pathogenic/Likely pathogenic ★★ same condition
- CTCF p.Arg368Cys Pathogenic ★★ same condition
- CTCF p.Pro378Leu Pathogenic/Likely pathogenic ★★ same condition
- CTCF p.Arg277Gln Uncertain significance ★★ ⚠ same condition
- CTCF p.Cys299Arg Uncertain significance ★★ ⚠ same condition
- CTCF p.Gly597Arg Uncertain significance ★★ ⚠ same condition
- CTCF p.Gly657Arg Uncertain significance ★★ ⚠ same condition
- CTCF p.Ile511Val Uncertain significance ★★ ⚠ 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-lys323 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown