TENM2

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

Basic information

Region (hg38): 5:166979028-168264157

Previous symbols: [ "ODZ2" ]

Links

ENSG00000145934

∙ NCBI:57451 ∙ OMIM:610119 ∙ HGNC:29943 ∙ Uniprot:Q9NT68 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TENM2 gene.

Inborn genetic diseases (108 variants)
not provided (13 variants)
not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TENM2 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				4 clinvar	2 clinvar	6
missense			108 clinvar	4 clinvar	1 clinvar	113
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
splice region ? Intron variants in splice region, excluding donor/acceptor (+/-2bp)					1	1
non coding ? UTR, intron and other, non coding variants				1 clinvar		1
Total	0	0	109	9	3

Variants in TENM2

This is a list of pathogenic ClinVar variants found in the TENM2 region.

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

Position	Phenotype	Significance	ClinVar
5-167284857-G-A		Likely benign (Feb 01, 2023)	2656025
5-167284862-C-T	not specified	Uncertain significance (Dec 20, 2023)	3175853
5-167284895-T-C	not specified	Uncertain significance (Jul 06, 2021)	3175869
5-167284980-C-T	not specified	Uncertain significance (Jul 12, 2022)	2301008
5-167284988-C-T	not specified	Uncertain significance (Sep 29, 2023)	3175848
5-167284989-A-G	not specified	Uncertain significance (Jan 31, 2024)	3175849
5-167285006-T-C	not specified	Uncertain significance (Oct 27, 2021)	2257550
5-167285037-G-A	not specified	Uncertain significance (Mar 03, 2022)	2228883
5-167375258-A-G	not specified	Uncertain significance (Aug 12, 2021)	2243687
5-167375311-G-A	not specified	Uncertain significance (Aug 08, 2022)	2213507
5-167375336-G-C	not specified	Uncertain significance (Jan 03, 2024)	3175857
5-167375350-C-A	not specified	Uncertain significance (Sep 09, 2021)	2358519
5-167375390-G-A	not specified	Uncertain significance (Aug 14, 2023)	2597314
5-167375399-G-T	not specified	Uncertain significance (Nov 06, 2023)	3175859
5-167375459-C-T	not specified	Uncertain significance (Aug 08, 2022)	2379415
5-167876060-C-T	not specified	Uncertain significance (Apr 12, 2022)	2204945
5-167952612-C-T	not specified	Uncertain significance (Dec 27, 2023)	3175878
5-167952662-C-G	not specified	Uncertain significance (Apr 20, 2023)	2529393
5-167952704-A-G	not specified	Uncertain significance (Oct 06, 2021)	2254106
5-167993034-G-A		Likely benign (Apr 01, 2022)	2656026
5-167993134-G-A	not specified	Uncertain significance (Jun 17, 2022)	2377731
5-167993144-C-T	not specified	Uncertain significance (Dec 09, 2023)	3175843
5-167993149-C-T	not specified	Uncertain significance (Jul 20, 2021)	2238470
5-167993171-C-T	not specified	Uncertain significance (Aug 16, 2022)	3175844
5-168047448-A-G	not specified	Uncertain significance (Jul 20, 2022)	2390502

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TENM2	protein_coding	protein_coding	ENST00000518659	29	979359

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	9.42e-9	124625	0	17	124642	0.0000682

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.30	1284	1.66e+3	0.772	0.000105	18201
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000101	0.0000980
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000101	0.0000973
Middle Eastern	0.00	0.00
South Asian	0.000138	0.000131
Other	0.00	0.00

dbNSFP

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}.;

Haploinsufficiency Scores

pHI: 0.255
hipred: Y
hipred_score: 0.623
ghis: 0.454

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2: N
essential_gene_gene_trap
gene_indispensability_pred
gene_indispensability_score

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Tenm2
Phenotype: vision/eye 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);

Gene ontology

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;cell-cell adhesion
Cellular component: nucleus;endoplasmic reticulum;Golgi apparatus;plasma membrane;integral component of plasma membrane;PML body;cell junction;filopodium;dendrite;growth cone;neuron projection;dendritic spine;synapse;postsynaptic membrane
Molecular function: calcium ion binding;protein homodimerization activity;protein heterodimerization activity;cell adhesion molecule binding