TENM2

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

Basic information

Region (hg38): 5:166979029-168264157

Previous symbols: [ "ODZ2" ]

Links

ENSG00000145934NCBI:57451OMIM:610119HGNC:29943Uniprot:Q9NT68AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

  • not_specified (353 variants)
  • not_provided (16 variants)
  • Pyloric_stenosis (1 variants)
  • Esophageal_atresia (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. These statistics are base on transcript: NM_001395460.1. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
9
clinvar
2
clinvar
11
missense
350
clinvar
6
clinvar
1
clinvar
357
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total 0 0 351 15 3
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TENM2protein_codingprotein_codingENST00000518659 29979359
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.009.42e-91246250171246420.0000682
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.3012841.66e+30.7720.00010518201
Missense in Polyphen414642.590.644266854
Synonymous-0.4077016871.020.00004685510
Loss of Function8.49131080.1200.000005741243

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001010.0000980
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.0001010.0000973
Middle Eastern0.000.00
South Asian0.0001380.000131
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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