CNTN2 p.Pro780=
c.2340C>G · rs975647789 · VCV474476
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00254%, nfe)
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 0.25 | GERP -4.4, phastCons 0.98 |
| Overall | ||
| CADD | 13.09 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00254%
European (non-Finnish) · 30/1,180,038 alleles
Filtering AF
0.0018%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00156%
Overall
0.00186%
30/1,613,680 alleles · very rare
exomes 26/1,461,462 · genomes 4/152,218 · joint denominator
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.Pro780=
- Coding
- c.2340C>G
- MANE Select
- NM_005076
- dbSNP
- rs975647789
- Type
- single nucleotide variant
- Location
- chr1:205069970 (GRCh38)
- Gene constraint
- LOEUF 0.542 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 86.13 · 5 PDB
- Residue 780
- the fibronectin type-iii 2 domain
Similar variants
- 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
- CNTN2 p.Ala263Thr 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-pro780 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown