CNTNAP3B

protein-coding

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

Gene summary

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]

MANE transcript

NM_001201380.3

Inheritance

—

ClinVar variants

U:303B:27

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.27

Max pathogenic AF

—

Genomic locus

chr9:41,890,314-42,129,510

External References & Databases

Ensembl (ENSG00000154529)

Transcript & Mutation Effects

hg38 • Region Span ~239.2 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 CNTNAP3B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 319

not providedTotal: 13

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001201380.3. 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			1 clinvar	6 clinvar	1 clinvar	8
missense			302 clinvar	19 clinvar		321
nonsense						0
start loss						0
frameshift					1 clinvar	1
splice donor/acceptor (+/-2bp)						0
Total	0	0	303	25	2	330

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 31 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001201380.3	RefSeq	NP_001188309.2	24	MANE Select
ENST00000377561.7	Ensembl	ENSP00000478671.2	24	MANE Select
ENST00000276974.7	Ensembl	ENSP00000276974.5	8	Standard
ENST00000276974.8	Ensembl	ENSP00000276974.5	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell adhesion

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000377564
Coding exons: 24
Length: 239148
Individuals with no LoFs: 125459
Homozygous LoFs: 2
Heterozygous LoFs: 53
Defined: 125514
p: 0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-2.48	423	302	1.40	0.0000161	8020
Missense (PolyPhen)		107	75.159	1.4236		2149
Synonymous	-2.49	162	126	1.28	0.00000768	2512
Loss of Function	-1.39	38	29.8	1.27	0.00000163	699

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00060	0.00049	rare
Latino/Admixed American	0.00028	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00024	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00020	0.00018	rare
South Asian	0.00065	0.00049	rare
Other	0.00021	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.154

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High