TENM1

protein-coding

teneurin transmembrane protein 1, the group of Teneurin transmembrane protein family

Gene summary

The protein encoded by this gene belongs to the tenascin family and teneurin subfamily. It is expressed in the neurons and may function as a cellular signal transducer. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]

Previous symbols:

ODZ3
TNM
ODZ1

MANE transcript

NM_001163278.2

Inheritance

AD, XL, AR

ClinVar variants

P:1U:657B:59

Top phenotype

Microphthalmia, isolated, with coloboma 9

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chrX:124,375,903-125,204,312

External References & Databases

Ensembl (ENSG00000009694)

Transcript & Mutation Effects

hg38 • Region Span ~828.4 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

isolated congenital anosmiaSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007137

Submitter: Orphanet

cerebral palsyLIMITED

Inheritance Pattern: XL

Disease ID:MONDO:0006497

Submitter: Ambry Genetics

anosmiaLIMITED

Inheritance Pattern: XL

Disease ID:MONDO:0010528

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Microphthalmia, isolated, with coloboma 9AR

Manifestation: Ophthalmologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 22766609

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TENM1 variants in ClinVar

6 Conditions Cataloged

not specifiedTotal: 241

not providedTotal: 43

TENM1-related disorderTotal: 37

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

Moyamoya angiopathyTotal: 1

Sensorineural hearing loss disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001163278.2. 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			87 clinvar	24 clinvar	15 clinvar	126
missense		1 clinvar	480 clinvar	15 clinvar	5 clinvar	501
nonsense			38 clinvar			38
start loss			1 clinvar			1
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			50 clinvar			50
Total	0	1	657	39	20	717

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001163278.2	RefSeq	NP_001156750.1	32	MANE Select
ENST00000422452.4	Ensembl	ENSP00000403954.4	32	MANE Select
NM_001163279.1	RefSeq	NP_001156751.1	32	Standard
NM_014253.3	RefSeq	NP_055068.2	31	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase III
immune response
heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules
neuropeptide signaling pathway
nervous system development

Molecular Function

heparin binding
protein homodimerization activity
protein heterodimerization activity
cell adhesion molecule binding

Cellular Component

extracellular region
nucleus
cytoplasm
endoplasmic reticulum
Golgi apparatus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000422452
Coding exons: 32
Length: 587914
Individuals with no LoFs: 125733
Homozygous LoFs: 4
Heterozygous LoFs: 6
Defined: 125743
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.43	748	1.06e+3	0.704	0.0000818	17972
Missense (PolyPhen)		144	295.8	0.48681		4711
Synonymous	0.358	394	403	0.977	0.0000319	5329
Loss of Function	7.71	10	88.1	0.114	0.00000701	1445

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000073	0.000058	rare
Ashkenazi Jewish	0.00013	0.000099	rare
East Asian	0.000073	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000074	0.000053	rare
South Asian	0	0.0	absent
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. May function as a cellular signal transducer (By similarity). {ECO:0000250}.; FUNCTION: Ten-1 intracellular domain: Induces gene transcription activation. {ECO:0000250}.;

Recessive Scores

pRec: 0.108

Intolerance Scores

RVIS EVS: -3.46
RVIS percentile EVS: 0.36

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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