TENM2

protein-coding

teneurin transmembrane protein 2, the group of Teneurin transmembrane protein family

Gene summary

Enables cell adhesion molecule binding activity and signaling receptor binding activity. Involved in retrograde trans-synaptic signaling by trans-synaptic protein complex. Located in cell-cell junction and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

ODZ2

MANE transcript

NM_001395460.1

Inheritance

—

ClinVar variants

U:415B:18

Top phenotype

Pyloric stenosis

gnomAD constraint

pLI —, LoF o/e 0.12

Max pathogenic AF

—

Genomic locus

chr5:166,979,029-168,264,157

External References & Databases

Ensembl (ENSG00000145934)

Transcript & Mutation Effects

hg38 • Region Span ~1,285.1 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 TENM2 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 406

not providedTotal: 20

Pyloric stenosisTotal: 1

Neurodevelopmental disorderTotal: 1

Esophageal atresiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001395460.1. 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	9 clinvar	2 clinvar	13
missense			408 clinvar	6 clinvar	1 clinvar	415
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	415	15	3	433

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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_001395460.1	RefSeq	NP_001382389.1	29	MANE Select
ENST00000518659.6	Ensembl	ENSP00000429430.1	29	MANE Select
NM_001080428.3	RefSeq	NP_001073897.2	25	Standard
NM_001122679.2	RefSeq	NP_001116151.1	29	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of transcription by RNA polymerase II
heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules
signal transduction
neuron development
positive regulation of filopodium assembly

Molecular Function

calcium ion binding
protein homodimerization activity
protein heterodimerization activity
cell adhesion molecule binding

Cellular Component

nucleus
endoplasmic reticulum
Golgi apparatus
plasma membrane
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000518659
Coding exons: 29
Length: 979359
Individuals with no LoFs: 124625
Homozygous LoFs: 0
Heterozygous LoFs: 17
Defined: 124642
p: 0.0000682

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.30	1284	1.66e+3	0.772	0.000105	18201
Missense (PolyPhen)		414	642.59	0.64426		6854
Synonymous	-0.407	701	687	1.02	0.0000468	5510
Loss of Function	8.49	13	108	0.120	0.00000574	1243

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000067	0.000065	rare
Latino/Admixed American	0.000033	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00010	0.000097	rare
South Asian	0.00014	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in neural development, regulating the establishment of proper connectivity within the nervous system. Promotes the formation of filopodia and enlarged growth cone in neuronal cells. Induces homophilic cell-cell adhesion (By similarity). May function as a cellular signal transducer. {ECO:0000250, ECO:0000269|PubMed:21724987}.; FUNCTION: Ten-2 intracellular domain: Induces gene transcription inhibition. {ECO:0000250}.;

Essentials

Essential (CRISPR2): N

Gene Damage Prediction

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