TNN
protein-codingtenascin N, the group of Tenascins
Gene summary
Predicted to enable integrin binding activity. Involved in positive regulation of sprouting angiogenesis; regulation of cell adhesion; and regulation of cell migration. Located in extracellular matrix. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~80.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TNN variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_022093.2. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 2 | 3 | |||
| missense | 210 | 11 | 2 | 223 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 214 | 13 | 2 | 229 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_071376.1 | 18 | MANE Select | |
| Ensembl | ENSP00000239462.4 | 18 | MANE Select | |
| Ensembl | ENSP00000480895.1 | 16 | Standard | |
| Ensembl | ENSP00000530513.1 | 16 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- PI3K-Akt signaling pathway - Homo sapiens (human)
- ECM-receptor interaction - Homo sapiens (human)
- Focal adhesion - Homo sapiens (human)
- MicroRNAs in cancer - Homo sapiens (human)
- Human papillomavirus infection - Homo sapiens (human)
Biological Process
- osteoblast development
- cell-matrix adhesion
- axonogenesis
- negative regulation of osteoblast proliferation
- negative regulation of osteoblast differentiation
Molecular Function
- molecular_function
- integrin binding
- identical protein binding
Cellular Component
- cellular_component
- cell surface
- extracellular matrix
- neuronal cell body
- CA3 pyramidal cell dendrite
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000239462
- Coding exons
- 18
- Length
- 80209
- Individuals with no LoFs
- 125478
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 268
- Defined
- 125748
- p
- 0.00107
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.539 | 824 | 782 | 1.05 | 0.0000467 | 8465 |
| Missense (PolyPhen) | 272 | 273.75 | 0.99359 | 3142 | ||
| Synonymous | -0.250 | 329 | 323 | 1.02 | 0.0000215 | 2544 |
| Loss of Function | 1.27 | 49 | 59.6 | 0.822 | 0.00000297 | 643 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0011 | 0.00092 | notable |
| Latino/Admixed American | 0.00061 | 0.00061 | rare |
| Ashkenazi Jewish | 0.0051 | 0.0050 | notable |
| East Asian | 0.0020 | 0.0019 | notable |
| Finnish | 0.00037 | 0.00037 | rare |
| European (Non-Finnish) | 0.00094 | 0.00093 | rare |
| South Asian | 0.00089 | 0.00082 | rare |
| Other | 0.0016 | 0.0016 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Extracellular matrix protein that seems to be a ligand for ITGA8:ITGB1, ITGAV:ITGB1 and ITGA4:ITGB1 (By similarity) (PubMed:17909022). Involved in neurite outgrowth and cell migration in hippocampal explants (By similarity). During endochondral bone formation, inhibits proliferation and differentiation of proteoblasts mediated by canonical WNT signaling (By similarity). In tumors, stimulates angiogenesis by elongation, migration and sprouting of endothelial cells (PubMed:19884327). Expressed in most mammary tumors, may facilitate tumorigenesis by supporting the migratory behavior of breast cancer cells (PubMed:17909022). {ECO:0000250|UniProtKB:Q80YX1, ECO:0000250|UniProtKB:Q80Z71, ECO:0000269|PubMed:17909022, ECO:0000269|PubMed:19884327}.;
Intolerance Scores
- LoFtool
- 0.767
- RVIS EVS
- 1.51
- RVIS percentile EVS
- 95.43
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.655
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | High | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |