TENM2
Basic information
Region (hg38): 5:166979029-168264157
Previous symbols: [ "ODZ2" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 11 | |||||
missense | 350 | 357 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
Total | 0 | 0 | 351 | 15 | 3 |
GnomAD
Source:
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:
- 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