TNN

tenascin N, the group of Tenascins

Basic information

Region (hg38): 1:175067832-175148075

Links

ENSG00000120332 ∙ NCBI:63923 ∙ OMIM:617472 ∙ HGNC:22942 ∙ Uniprot:Q9UQP3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Inborn genetic diseases (56 variants)
• not provided (2 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.

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						0
missense			55	1	1	57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	55	1	1

Variants in TNN

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

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

Position	Type	Phenotype	Significance	ClinVar
1-175077491-C-A		not specified	Uncertain significance (Mar 24, 2023)
1-175077522-A-G		not specified	Uncertain significance (Jan 20, 2023)
1-175077528-A-C		not specified	Uncertain significance (Oct 26, 2022)
1-175077572-A-C		not specified	Uncertain significance (Feb 28, 2024)
1-175077750-G-A		not specified	Uncertain significance (Oct 02, 2023)
1-175077784-G-A		not specified	Uncertain significance (Sep 21, 2021)
1-175077807-G-A		not specified	Uncertain significance (Apr 12, 2022)
1-175079335-C-A		not specified	Uncertain significance (Aug 12, 2021)
1-175079444-C-A		not specified	Uncertain significance (Feb 27, 2024)
1-175079444-C-T		not specified	Uncertain significance (May 25, 2023)
1-175079521-C-A		not specified	Uncertain significance (Oct 05, 2022)
1-175079545-G-A		not specified	Uncertain significance (Nov 01, 2021)
1-175079594-T-C		not specified	Likely benign (Jan 10, 2023)
1-175079611-G-A		not specified	Uncertain significance (Mar 02, 2023)
1-175079667-C-G		not specified	Uncertain significance (Apr 22, 2022)
1-175079698-T-A		not specified	Uncertain significance (Mar 05, 2024)
1-175080169-C-A		not specified	Uncertain significance (Jan 23, 2024)
1-175080244-A-T		not specified	Uncertain significance (Jan 30, 2024)
1-175080249-T-C		not specified	Uncertain significance (Jul 05, 2023)
1-175080256-T-C		not specified	Uncertain significance (Dec 19, 2023)
1-175080279-G-A		not specified	Uncertain significance (Jul 09, 2021)
1-175083751-C-A		not specified	Uncertain significance (Jan 30, 2024)
1-175083765-G-T		not specified	Uncertain significance (Jan 05, 2022)
1-175083863-A-G		not specified	Uncertain significance (Feb 11, 2022)
1-175083865-G-A		not specified	Uncertain significance (Aug 22, 2022)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

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

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