CNTN2 p.Phe264=
c.792T>C · rs183799891 · VCV2875852
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
epilepsy, familial adult myoclonic, 5
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 -1.9 | GERP -4.1 |
| Overall | ||
| CADD | 8.228 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
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
- CNTN2
- Protein
- p.Phe264=
- Coding
- c.792T>C
- MANE Select
- NM_005076
- dbSNP
- rs183799891
- Type
- single nucleotide variant
- Location
- chr1:205059677 (GRCh38)
- Gene constraint
- LOEUF 0.542 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 86.13 · 5 PDB
- Residue 264
- the ig-like c2-type 3 domain; a β-strand
Similar variants
- CNTN2 p.Phe264Leu Uncertain significance ★ ⚠ same residue
- CNTN2 c.1241-1G>C Likely pathogenic ★★ same condition
- CNTN2 c.2432-2A>G Likely pathogenic ★★ same condition
- CNTN2 p.Arg140Ter Pathogenic/Likely pathogenic ★★ same condition
- CNTN2 p.Arg314Ter Pathogenic ★★ same condition
- CNTN2 p.Trp731Ter Pathogenic/Likely pathogenic ★★ same condition
- CNTN2 c.2196+5G>A Uncertain significance ★★ same condition
- CNTN2 p.Ala230Val 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/cntn2-p-phe264 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown