CNTNAP3C

Chr 9

contactin associated protein family member 3C

The protein is predicted to function in cell adhesion and is located in cellular membranes. However, there is currently insufficient clinical data available to establish definitive disease associations, inheritance patterns, or phenotypic consequences of CNTNAP3C mutations. This gene requires further research to determine its role in human disease.

ResearchSummary from RefSeq

Predicted to be involved in nervous system development and signal transduction. Predicted to be located in membrane. Predicted to be active in plasma membrane and synapse. [provided by Alliance of Genome Resources, Jun 2026]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

—

LOEUF

Multiple*

Mechanism· predicted

Some data sources returned errors (2)

gnomad: Error: Gene not found

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD

Constraint data not available from gnomAD.

Background carrier burden — how many people carry a rare variant somewhere in CNTNAP3C?

gnomAD v4 · ~686k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 2,200

16 rare PASS variants

Rare truncating (LoF)

1 in 14,000

4 rare PASS variants

Rare synonymous (reference)

1 in 8,700

13 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for CNTNAP3C. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 7 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~527k	1 in 3,500	1 in 59,000
South Asian	~39k	1 in 400	1 in 1,400
Remaining (unassigned)	~28k	1 in 1,200	1 in 5,300
East Asian	~20k	none seen	≈ 1 in 15,000
Admixed American	~19k	≈ 1 in 8,900	none seen
Ashkenazi Jewish	~12k	1 in 1,200	1 in 980
Middle Eastern	~1,972	≈ 1 in 1,900	none seen

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 0 of 9 coding exons well covered in gnomAD exomes; exons 2, 3, 4, 5, 6 and 3 more poorly covered; exon 1 marginal. Genomes: 0 of 9 (exons 1, 2, 3, 4, 5 and 4 more below).? see exons ↓