CNTN3

protein-coding

contactin 3, the group of I-set domain containing|Contactins

Gene summary

Predicted to be involved in cell adhesion. Predicted to be located in extracellular region and plasma membrane. Predicted to be active in neuron projection. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

PANG

MANE transcript

NM_020872.3

Inheritance

—

ClinVar variants

U:133B:24

Top phenotype

CNTN3-related disorder

gnomAD constraint

pLI —, LoF o/e 0.35

Max pathogenic AF

—

Genomic locus

chr3:74,262,568-74,614,659

External References & Databases

Ensembl (ENSG00000113805)

Transcript & Mutation Effects

hg38 • Region Span ~352.1 kb

Loading mutation effect viewer...

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 CNTN3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 124

not providedTotal: 19

CNTN3-related disorderTotal: 19

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020872.3. 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			2 clinvar	7 clinvar	2 clinvar	11
missense			127 clinvar	10 clinvar	5 clinvar	142
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	133	17	7	157

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020872.3	RefSeq	NP_065923.1	22	MANE Select
ENST00000263665.7	Ensembl	ENSP00000263665.6	22	MANE Select
NM_001393376.1	RefSeq	NP_001380305.1	22	Standard
ENST00000906976.1	Ensembl	ENSP00000577035.1	19	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Post-translational modification: synthesis of GPI-anchored proteins
Post-translational protein modification
Metabolism of proteins

Biological Process

cell adhesion
nervous system development

Cellular Component

extracellular region
plasma membrane
anchored component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000263665
Coding exons: 22
Length: 258573
Individuals with no LoFs: 125718
Homozygous LoFs: 0
Heterozygous LoFs: 29
Defined: 125747
p: 0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.32	460	547	0.841	0.0000275	6661
Missense (PolyPhen)		164	242.34	0.67673		2905
Synonymous	-0.409	207	200	1.04	0.0000106	2010
Loss of Function	4.37	18	52.0	0.346	0.00000257	649

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0.00040	0.00020	rare
East Asian	0.000062	0.000054	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.00020	0.00020	rare
Other	0.00034	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Contactins mediate cell surface interactions during nervous system development. Has some neurite outgrowth-promoting activity (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.430

Intolerance Scores

RVIS EVS: 0.32
RVIS percentile EVS: 72.8

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.189

Gene Damage Prediction

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