CNTNAP1
Chr 17ARcontactin associated protein 1
Also known as: CASPR, CHN3, CNTNAP, NRXN4, P190
The protein is required for radial and longitudinal organization of myelinated axons and demarcates the paranodal region of the axo-glial junction, forming functional domains critical for saltatory conduction of nerve impulses. Mutations cause hypomyelinating neuropathy, congenital, 3 and lethal congenital contracture syndrome 7 through autosomal recessive inheritance. The pathogenicity results from disrupted signaling between axons and myelinating glial cells, impairing proper myelination and nerve conduction.
Primary Disease Associations & Inheritance
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Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
More LoF-intolerant than ~75% of genes
Highly missense-constrained (top ~0.1%)
Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.
The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.
ClinVar Variant Classifications
551 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 9 | 1 | 24 | 0 | 34 |
Likely Pathogenic | 8 | 4 | 6 | 0 | 18 |
VUS | 2 | 228 | 8 | 2 | 240 |
Likely Benign | 0 | 5 | 74 | 106 | 185 |
Benign | 0 | 1 | 41 | 9 | 51 |
Conflicting | — | 9 | |||
| Total | 19 | 239 | 153 | 117 | 537 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
CNTNAP1 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools