TENM3
Basic information
Region (hg38): 4:182143987-182803024
Previous symbols: [ "ODZ3" ]
Links
Phenotypes
GenCC
Source:
- 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:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Microphthalmia/coloboma 9 | AR | 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 | Craniofacial; Neurologic; Ophthalmologic | 22766609; 29753094; 30513139 |
ClinVar
This is a list of variants' phenotypes submitted to
- 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 | 33 | 87 | |||
missense | 165 | 15 | 186 | |||
nonsense | 2 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 1 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 3 | 7 | 4 | 14 | ||
non coding | 23 | 79 | 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) | |||
4-182323774-G-A | Benign (Oct 18, 2020) | |||
4-182324032-A-G | Likely benign (Jun 20, 2018) | |||
4-182324056-G-A | Likely benign (May 23, 2023) | |||
4-182324110-T-G | Inborn genetic diseases | Uncertain significance (Feb 08, 2022) | ||
4-182324138-T-A | Inborn genetic diseases | Uncertain significance (Jan 06, 2023) | ||
4-182324215-T-A | Inborn genetic diseases | Uncertain significance (Apr 27, 2024) | ||
4-182324225-A-G | Inborn genetic diseases | Uncertain significance (Dec 20, 2023) | ||
4-182346337-T-A | Benign (Jun 26, 2018) | |||
4-182346575-TA-T | Benign (May 17, 2021) | |||
4-182346575-TAA-T | Likely benign (May 16, 2021) | |||
4-182346631-C-CT | Benign (Feb 14, 2022) | |||
4-182346665-C-G | Inborn genetic diseases | Uncertain significance (Mar 06, 2023) | ||
4-182346680-G-A | Inborn genetic diseases | Uncertain significance (Mar 06, 2023) | ||
4-182346710-G-T | Likely benign (Dec 09, 2023) | |||
4-182346721-G-T | Benign (Dec 09, 2023) | |||
4-182346733-C-T | Benign (Jan 23, 2024) | |||
4-182346789-C-G | Inborn genetic diseases | Uncertain significance (Mar 30, 2024) | ||
4-182346812-A-G | Inborn genetic diseases | Uncertain significance (Jul 09, 2021) | ||
4-182346820-T-C | Likely benign (Aug 09, 2023) | |||
4-182346832-G-T | TENM3-related disorder | Likely benign (Sep 29, 2022) | ||
4-182346857-C-T | Benign (Jan 04, 2023) | |||
4-182346858-T-A | Inborn genetic diseases | Uncertain significance (Dec 14, 2023) | ||
4-182346948-T-C | Likely benign (Jun 28, 2022) | |||
4-182346995-C-CG | Benign (Sep 04, 2018) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
TENM3 | protein_coding | protein_coding | ENST00000511685 | 27 | 659038 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 0.000452 | 124610 | 0 | 32 | 124642 | 0.000128 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 3.30 | 1191 | 1.56e+3 | 0.765 | 0.0000945 | 17631 |
Missense in Polyphen | 154 | 218.2 | 0.70578 | 1933 | ||
Synonymous | 0.112 | 623 | 627 | 0.994 | 0.0000418 | 5310 |
Loss of Function | 8.11 | 21 | 115 | 0.183 | 0.00000625 | 1331 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000212 | 0.000212 |
Ashkenazi Jewish | 0.000497 | 0.000497 |
East Asian | 0.0000582 | 0.0000556 |
Finnish | 0.000139 | 0.000139 |
European (Non-Finnish) | 0.0000995 | 0.0000973 |
Middle Eastern | 0.0000582 | 0.0000556 |
South Asian | 0.000100 | 0.0000980 |
Other | 0.000497 | 0.000496 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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