CNTNAP3

protein-coding

contactin associated protein family member 3, the group of Contactin associated protein family

Gene summary

The protein encoded by this gene belongs to the NCP family of cell-recognition molecules. This family represents a distinct subgroup of the neurexins. NCP proteins mediate neuron-glial interactions in vertebrates and glial-glial contact in invertebrates. The protein encoded by this gene may play a role in cell recognition within the nervous system. Alternatively spliced transcript variants encoding different isoforms have been described but their biological nature has not been determined. [provided by RefSeq, Jul 2008]

MANE transcript

NM_033655.5

Inheritance

—

ClinVar variants

U:196B:18

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.55

Max pathogenic AF

—

Genomic locus

chr9:39,064,710-39,288,315

External References & Databases

Ensembl (ENSG00000106714)

Transcript & Mutation Effects

hg38 • Region Span ~223.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CNTNAP3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 205

not providedTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_033655.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				4 clinvar	1 clinvar	5
missense			194 clinvar	13 clinvar		207
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	196	17	1	214

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 45 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_033655.5	RefSeq	NP_387504.2	24	MANE Select
ENST00000297668.11	Ensembl	ENSP00000297668.6	24	MANE Select
NM_001393379.1	RefSeq	NP_001380308.1	23	Standard
ENST00000358144.6	Ensembl	ENSP00000350863.2	18	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell adhesion
cell recognition

Cellular Component

extracellular region
plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000297668
Coding exons: 24
Length: 215549
Individuals with no LoFs: 125489
Homozygous LoFs: 1
Heterozygous LoFs: 113
Defined: 125603
p: 0.000454

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.146	518	527	0.982	0.0000302	8224
Missense (PolyPhen)		128	150.66	0.84957		2910
Synonymous	-1.57	243	214	1.14	0.0000137	2569
Loss of Function	2.82	25	45.5	0.549	0.00000249	705

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00026	0.00025	rare
Latino/Admixed American	0.00081	0.00081	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00087	0.00082	rare
Finnish	0.0014	0.0014	notable
European (Non-Finnish)	0.00020	0.00019	rare
South Asian	0.00029	0.00029	rare
Other	0.0010	0.00098	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0943

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.536

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium