TENM4

teneurin transmembrane protein 4, the group of MicroRNA protein coding host genes|Teneurin transmembrane protein family

Basic information

Region (hg38): 11:78652828-79441030

Previous symbols: [ "ODZ4" ]

Links

ENSG00000149256 ∙ NCBI:26011 ∙ OMIM:610084 ∙ HGNC:29945 ∙ Uniprot:Q6N022 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• tremor, hereditary essential, 5 (Strong), mode of inheritance: AD
• tremor, hereditary essential, 5 (Moderate), mode of inheritance: AD
• tremor, hereditary essential, 5 (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Tremor, hereditary essential, 5	AD	General	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	Neurologic	26188006

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TENM4 gene.

• Inborn genetic diseases (134 variants)
• not provided (109 variants)
• Tremor, hereditary essential, 5 (23 variants)
• not specified (8 variants)
• TENM4-related condition (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TENM4 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	27	15	43
missense			176	8	15	199
nonsense						0
start loss						0
frameshift		1	1			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1		1	2
non coding					1	1
Total	0	1	178	35	31

Variants in TENM4

This is a list of pathogenic ClinVar variants found in the TENM4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-78658105-C-T		not specified	Uncertain significance (Mar 29, 2023)
11-78658110-T-C		not specified	Uncertain significance (Feb 21, 2024)
11-78658132-C-T		not specified	Uncertain significance (Aug 15, 2023)
11-78658157-G-A		TENM4-related disorder	Likely benign (Jun 09, 2020)
11-78658167-A-C		not specified	Uncertain significance (Feb 12, 2024)
11-78658170-C-T		TENM4-related disorder	Likely benign (Dec 31, 2019)
11-78658216-G-A		not specified	Uncertain significance (Feb 28, 2024)
11-78658253-G-A			Likely benign (Nov 01, 2023)
11-78658269-C-T		not specified	Uncertain significance (Dec 13, 2023)
11-78658303-G-A		not specified	Uncertain significance (Dec 28, 2023)
11-78658338-G-A			Uncertain significance (Apr 01, 2022)
11-78658357-C-T		TENM4-related disorder	Benign (Jun 26, 2019)
11-78658358-G-A			Benign/Likely benign (Jan 01, 2024)
11-78658366-G-A		not specified	Uncertain significance (Jan 04, 2024)
11-78658368-T-C			Benign (Nov 01, 2023)
11-78658384-G-A		not specified	Uncertain significance (Oct 10, 2023)
11-78658429-C-T		Tremor, hereditary essential, 5	Uncertain significance (Sep 27, 2021)
11-78658435-C-T			Benign (Dec 31, 2019)
11-78658440-T-C		not specified	Uncertain significance (May 25, 2022)
11-78658455-C-T			Benign (Dec 31, 2019)
11-78658456-G-A		not specified	Uncertain significance (Nov 16, 2023)
11-78658528-C-A		not specified	Uncertain significance (Feb 15, 2023)
11-78658528-C-T		TENM4-related disorder • not specified	Benign/Likely benign (Feb 15, 2023)
11-78658546-G-C			Uncertain significance (Jul 01, 2022)
11-78658552-T-A		not specified	Uncertain significance (Aug 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TENM4	protein_coding	protein_coding	ENST00000278550	30	788117

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.10e-9	124637	0	13	124650	0.0000521

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.73	1341	1.65e+3	0.811	0.000105	18142
Missense in Polyphen		308	483.35	0.63722		5101
Synonymous	2.38	601	680	0.884	0.0000445	5534
Loss of Function	8.51	11	105	0.105	0.00000538	1217

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.0000933	0.0000928
European (Non-Finnish)	0.0000622	0.0000619
Middle Eastern	0.000111	0.000111
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in neural development, regulating the establishment of proper connectivity within the nervous system. Plays a role in the establishment of the anterior-posterior axis during gastrulation. Regulates the differentiation and cellular process formation of oligodendrocytes and myelination of small- diameter axons in the central nervous system (CNS) (PubMed:26188006). Promotes activation of focal adhesion kinase. May function as a cellular signal transducer (By similarity). {ECO:0000250|UniProtKB:Q3UHK6, ECO:0000269|PubMed:26188006}.
• Disease: DISEASE: Tremor, hereditary essential 5 (ETM5) [MIM:616736]: A common movement disorder mainly characterized by postural tremor of the arms. Head, legs, trunk, voice, jaw, and facial muscles also may be involved. The condition can be aggravated by emotions, hunger, fatigue and temperature extremes, and may cause a functional disability or even incapacitation. Inheritance is autosomal dominant. {ECO:0000269|PubMed:26188006}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Intolerance Scores

• rvis_EVS: -1.7
• rvis_percentile_EVS: 2.59

Haploinsufficiency Scores

• pHI: 0.595
• hipred: Y
• hipred_score: 0.683
• ghis: 0.535

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tenm4
• Phenotype: growth/size/body region phenotype; cellular phenotype; skeleton phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: tenm4
• Affected structure: motor neuron
• Phenotype tag: abnormal
• Phenotype quality: branchiness

Gene ontology

• Biological process: gastrulation with mouth forming second;heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules;signal transduction;regulation of myelination;positive regulation of myelination;central nervous system myelin formation;neuron development;positive regulation of oligodendrocyte differentiation;cardiac muscle cell proliferation;cardiac cell fate specification;positive regulation of gastrulation
• Cellular component: nucleus;cytoplasm;plasma membrane;integral component of plasma membrane;neuron projection
• Molecular function: protein homodimerization activity;protein heterodimerization activity;cell adhesion molecule binding