TENM3

teneurin transmembrane protein 3, the group of MicroRNA protein coding host genes|Teneurin transmembrane protein family

Basic information

Region (hg38): 4:182143987-182803024

Previous symbols: [ "ODZ3" ]

Links

ENSG00000218336NCBI:55714OMIM:610083HGNC:29944Uniprot:Q9P273AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • microphthalmia, isolated, with coloboma 9 (Strong), mode of inheritance: AR
  • microphthalmia, isolated, with coloboma 9 (Moderate), mode of inheritance: AR
  • microphthalmia, isolated, with coloboma (Supportive), mode of inheritance: AD
  • microphthalmia, isolated, with coloboma 9 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Microphthalmia/coloboma 9ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Neurologic; Ophthalmologic22766609; 29753094; 30513139

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TENM3 gene.

  • Microphthalmia, isolated, with coloboma 9 (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TENM3 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
54
clinvar
33
clinvar
87
missense
2
clinvar
165
clinvar
15
clinvar
4
clinvar
186
nonsense
2
clinvar
2
start loss
0
frameshift
0
inframe indel
1
clinvar
1
splice donor/acceptor (+/-2bp)
0
splice region
3
7
4
14
non coding
1
clinvar
23
clinvar
79
clinvar
103
Total 2 2 167 92 116

Variants in TENM3

This is a list of pathogenic ClinVar variants found in the TENM3 region.

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

Position Type Phenotype Significance ClinVar
4-182323716-C-T Benign (Jun 29, 2018)1280400
4-182323774-G-A Benign (Oct 18, 2020)1290374
4-182324032-A-G Likely benign (Jun 20, 2018)748419
4-182324056-G-A Likely benign (May 23, 2023)2888899
4-182324110-T-G Inborn genetic diseases Uncertain significance (Feb 08, 2022)2269141
4-182324138-T-A Inborn genetic diseases Uncertain significance (Jan 06, 2023)2474062
4-182324215-T-A Inborn genetic diseases Uncertain significance (Apr 27, 2024)3325340
4-182324225-A-G Inborn genetic diseases Uncertain significance (Dec 20, 2023)3175890
4-182346337-T-A Benign (Jun 26, 2018)1263794
4-182346575-TA-T Benign (May 17, 2021)1256668
4-182346575-TAA-T Likely benign (May 16, 2021)1326030
4-182346631-C-CT Benign (Feb 14, 2022)1899079
4-182346665-C-G Inborn genetic diseases Uncertain significance (Mar 06, 2023)3175894
4-182346680-G-A Inborn genetic diseases Uncertain significance (Mar 06, 2023)2459041
4-182346710-G-T Likely benign (Dec 09, 2023)718908
4-182346721-G-T Benign (Dec 09, 2023)718909
4-182346733-C-T Benign (Jan 23, 2024)774445
4-182346789-C-G Inborn genetic diseases Uncertain significance (Mar 30, 2024)3325330
4-182346812-A-G Inborn genetic diseases Uncertain significance (Jul 09, 2021)2249447
4-182346820-T-C Likely benign (Aug 09, 2023)754367
4-182346832-G-T TENM3-related disorder Likely benign (Sep 29, 2022)2178960
4-182346857-C-T Benign (Jan 04, 2023)2917693
4-182346858-T-A Inborn genetic diseases Uncertain significance (Dec 14, 2023)3175906
4-182346948-T-C Likely benign (Jun 28, 2022)1966835
4-182346995-C-CG Benign (Sep 04, 2018)1229849

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TENM3protein_codingprotein_codingENST00000511685 27659038
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.0004521246100321246420.000128
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.3011911.56e+30.7650.000094517631
Missense in Polyphen154218.20.705781933
Synonymous0.1126236270.9940.00004185310
Loss of Function8.11211150.1830.000006251331

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002120.000212
Ashkenazi Jewish0.0004970.000497
East Asian0.00005820.0000556
Finnish0.0001390.000139
European (Non-Finnish)0.00009950.0000973
Middle Eastern0.00005820.0000556
South Asian0.0001000.0000980
Other0.0004970.000496

dbNSFP

Source: dbNSFP

Function
FUNCTION: Involved in neural development by regulating the establishment of proper connectivity within the nervous system. Acts in both pre- and postsynaptic neurons in the hippocampus to control the assembly of a precise topographic projection: required in both CA1 and subicular neurons for the precise targeting of proximal CA1 axons to distal subiculum, probably by promoting homophilic cell adhesion. Required for proper dendrite morphogenesis and axon targeting in the vertebrate visual system, thereby playing a key role in the development of the visual pathway. Regulates the formation in ipsilateral retinal mapping to both the dorsal lateral geniculate nucleus (dLGN) and the superior colliculus (SC). May also be involved in the differentiation of the fibroblast-like cells in the superficial layer of mandibular condylar cartilage into chondrocytes. {ECO:0000250|UniProtKB:Q9WTS6}.;
Disease
DISEASE: Microphthalmia, isolated, with coloboma, 9 (MCOPCB9) [MIM:615145]: A disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues. Ocular abnormalities like opacities of the cornea and lens, scaring of the retina and choroid, and other abnormalities may also be present. Ocular colobomas are a set of malformations resulting from abnormal morphogenesis of the optic cup and stalk, and the fusion of the fetal fissure (optic fissure). {ECO:0000269|PubMed:22766609, ECO:0000269|PubMed:27103084}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Intolerance Scores

loftool
rvis_EVS
-3.46
rvis_percentile_EVS
0.36

Haploinsufficiency Scores

pHI
0.487
hipred
Y
hipred_score
0.685
ghis
0.615

Essentials

essential_gene_CRISPR
N
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
Tenm3
Phenotype
behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); 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);

Zebrafish Information Network

Gene name
tenm3
Affected structure
retinal ganglion cell
Phenotype tag
abnormal
Phenotype quality
process quality

Gene ontology

Biological process
homophilic cell adhesion via plasma membrane adhesion molecules;heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules;signal transduction;positive regulation of neuron projection development;camera-type eye morphogenesis;neuron development;regulation of homophilic cell adhesion
Cellular component
integral component of plasma membrane;membrane;axon;neuron projection
Molecular function
protein homodimerization activity;protein heterodimerization activity;cell adhesion molecule binding