CNTN2 p.Pro162=
c.486A>C · rs114050151 · VCV1170302
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 11.8%, sas) — too common for a highly-penetrant pathogenic allele
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 3 | GERP -2.5, phastCons 1 |
| Overall | ||
| CADD | 15.01 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
11.8%
South Asian · 10,737/90,842 alleles
Filtering AF
11.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 11.6%
Overall
3.45%
55,568/1,612,652 alleles · common
exomes 48,108/1,460,490 · genomes 7,460/152,162 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 11.8% | 8 |
| African / African-American | 8.23% | 12 |
| Finnishnot grpmax-eligible | 8.15% | 12 |
| Ashkenazi Jewishnot grpmax-eligible | 6.47% | 15 |
| Middle Eastern | 4.35% | 23 |
| Remaining individualsnot grpmax-eligible | 3.81% | 26 |
| Admixed American | 2.53% | 39 |
| European (non-Finnish) | 2.3% | 44 |
| East Asian | 0.618% | 162 |
| Amishnot grpmax-eligible | 0.11% | 910 |
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.Pro162=
- Coding
- c.486A>C
- MANE Select
- NM_005076
- dbSNP
- rs114050151
- Type
- single nucleotide variant
- Location
- chr1:205058662 (GRCh38)
- Gene constraint
- LOEUF 0.542 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 86.13 · 5 PDB
- Residue 162
- the ig-like c2-type 2 domain; a β-strand
Similar variants
- CNTN2 p.Pro162Ser 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-pro162 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown