TNN
Basic information
Region (hg38): 1:175067833-175148075
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (194 variants)
- not_provided (4 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNN gene is commonly pathogenic or not. These statistics are base on transcript: NM_000022093.2. 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 | 2 | |||||
missense | 185 | 195 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 185 | 10 | 2 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
TNN | protein_coding | protein_coding | ENST00000239462 | 18 | 80209 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.57e-28 | 0.00731 | 125478 | 2 | 268 | 125748 | 0.00107 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.539 | 824 | 782 | 1.05 | 0.0000467 | 8465 |
Missense in 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 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00172 | 0.00153 |
Ashkenazi Jewish | 0.00506 | 0.00497 |
East Asian | 0.00198 | 0.00190 |
Finnish | 0.000371 | 0.000370 |
European (Non-Finnish) | 0.000944 | 0.000932 |
Middle Eastern | 0.00198 | 0.00190 |
South Asian | 0.000892 | 0.000817 |
Other | 0.00164 | 0.00163 |
dbNSFP
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}.;
- Pathway
- 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);Focal Adhesion;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Extracellular matrix organization;ECM proteoglycans
(Consensus)
Intolerance Scores
- loftool
- 0.767
- rvis_EVS
- 1.51
- rvis_percentile_EVS
- 95.43
Haploinsufficiency Scores
- pHI
- 0.170
- hipred
- N
- hipred_score
- 0.231
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.655
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | High | High | High |
Primary Immunodeficiency | High | High | High |
Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Tnn
- Phenotype
Gene ontology
- Biological process
- osteoblast development;cell-matrix adhesion;axonogenesis;negative regulation of osteoblast proliferation;negative regulation of osteoblast differentiation;dendrite self-avoidance;negative regulation of canonical Wnt signaling pathway involved in osteoblast differentiation;negative regulation of neuron migration
- Cellular component
- cellular_component;cell surface;extracellular matrix;neuronal cell body;CA3 pyramidal cell dendrite;hippocampal mossy fiber expansion
- Molecular function
- molecular_function;integrin binding;identical protein binding