CNTN2 p.Arg64=
c.192G>A · VCV3642462
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00446%, eas)
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 0.56 | GERP -1.3, phastCons 0.99 |
| Overall | ||
| CADD | 7.061 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,884 alleles
Filtering AF
0.000739%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000276%
Overall
0.00131%
2/152,214 alleles · very rare
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
- CNTN2
- Protein
- p.Arg64=
- Coding
- c.192G>A
- MANE Select
- NM_005076
- Type
- single nucleotide variant
- Location
- chr1:205058042 (GRCh38)
- Gene constraint
- LOEUF 0.542 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 86.13 · 5 PDB
- Residue 64
- a disulfide bond; the ig-like c2-type 1 domain; a β-strand
Similar variants
- CNTN2 p.Arg64Trp Uncertain significance ★★ ⚠ same residue
- CNTN2 p.Arg64Gln 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
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-arg64 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown