TLN1

talin 1, the group of FERM domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 9:35696948-35732195

Previous symbols: [ "TLN" ]

Links

ENSG00000137076 ∙ NCBI:7094 ∙ OMIM:186745 ∙ HGNC:11845 ∙ Uniprot:Q9Y490 ∙ 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 TLN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TLN1 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				5	6	11
missense			74	1		75
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region				2	2	4
non coding						0
Total	0	1	75	6	6

Variants in TLN1

This is a list of pathogenic ClinVar variants found in the TLN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-35697804-C-T		not specified	Uncertain significance (Nov 09, 2023)
9-35697849-G-C		not specified	Uncertain significance (Apr 22, 2022)
9-35698343-C-G		not specified	Uncertain significance (Apr 16, 2024)
9-35698435-C-T		not specified	Uncertain significance (May 13, 2024)
9-35698480-T-C		not specified	Uncertain significance (Dec 22, 2023)
9-35698488-C-T			Likely benign (Jul 01, 2023)
9-35698615-A-G		Capillary leak syndrome	Likely pathogenic (-)
9-35700009-T-G		not specified	Uncertain significance (Apr 25, 2023)
9-35700020-C-T		not specified	Uncertain significance (Aug 08, 2023)
9-35700021-G-A		not specified	Uncertain significance (Mar 15, 2024)
9-35700038-C-T		not specified	Uncertain significance (May 18, 2023)
9-35700044-C-T		not specified	Uncertain significance (Mar 31, 2023)
9-35700193-T-C		not specified	Uncertain significance (Aug 15, 2023)
9-35700270-T-A		not specified	Uncertain significance (Jul 27, 2022)
9-35703573-C-T		not specified	Uncertain significance (Jan 04, 2022)
9-35703575-T-C		not specified	Uncertain significance (Nov 21, 2022)
9-35703663-T-C			Uncertain significance (Jan 22, 2024)
9-35703673-T-C		not specified	Uncertain significance (Nov 09, 2023)
9-35703789-T-C		not specified	Uncertain significance (Dec 30, 2023)
9-35703821-T-C		not specified	Uncertain significance (Jul 13, 2022)
9-35703848-A-G		not specified	Uncertain significance (Nov 03, 2023)
9-35704068-C-T		not specified	Uncertain significance (Jan 02, 2024)
9-35704088-G-A		not specified	Uncertain significance (Oct 20, 2021)
9-35704121-A-C		not specified	Uncertain significance (Jun 30, 2023)
9-35704462-G-A		not specified	Uncertain significance (Apr 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TLN1	protein_coding	protein_coding	ENST00000314888	56	35448

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	9.13e-15	125710	0	38	125748	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.67	970	1.48e+3	0.658	0.0000872	16375
Missense in Polyphen		358	660.06	0.54237		7348
Synonymous	1.47	535	580	0.922	0.0000337	5324
Loss of Function	9.84	10	132	0.0757	0.00000743	1422

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00139	0.00136
Finnish	0.000185	0.000185
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.00139	0.00136
South Asian	0.0000327	0.0000327
Other	0.000169	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably involved in connections of major cytoskeletal structures to the plasma membrane. High molecular weight cytoskeletal protein concentrated at regions of cell-substratum contact and, in lymphocytes, at cell-cell contacts (By similarity). {ECO:0000250}.
• Pathway: Platelet activation - Homo sapiens (human);Focal adhesion - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Integrin-mediated Cell Adhesion;Primary Focal Segmental Glomerulosclerosis FSGS;Focal Adhesion;XBP1(S) activates chaperone genes;Developmental Biology;Smooth Muscle Contraction;MAP2K and MAPK activation;Disease;Signal Transduction;erk and pi-3 kinase are necessary for collagen binding in corneal epithelia;ucalpain and friends in cell spread;integrin signaling pathway;mcalpain and friends in cell motility;rho cell motility signaling pathway;GRB2:SOS provides linkage to MAPK signaling for Integrins ;p130Cas linkage to MAPK signaling for integrins;Integrin alphaIIb beta3 signaling;Platelet Aggregation (Plug Formation);Muscle contraction;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Integrin;EGFR1;Integrin signaling;SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion;Hemostasis;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;Semaphorin interactions;Axon guidance;Signaling by RAS mutants;Signaling by high-kinase activity BRAF mutants;Signaling by moderate kinase activity BRAF mutants;Paradoxical activation of RAF signaling by kinase inactive BRAF;Nectin adhesion pathway;Signaling by BRAF and RAF fusions;Oncogenic MAPK signaling;Diseases of signal transduction;Signaling events mediated by focal adhesion kinase;amb2 Integrin signaling;Alpha4 beta1 integrin signaling events;Integrins in angiogenesis;RhoA signaling pathway (Consensus)

Recessive Scores

• pRec: 0.390

Intolerance Scores

• loftool: 0.268
• rvis_EVS: -3.42
• rvis_percentile_EVS: 0.37

Haploinsufficiency Scores

• pHI: 0.295
• hipred: Y
• hipred_score: 0.802
• ghis: 0.606

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.937

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Tln1
• Phenotype: muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; growth/size/body region phenotype; 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); digestive/alimentary phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype

Zebrafish Information Network

• Gene name: tln1
• Affected structure: cardiac muscle cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: platelet degranulation;muscle contraction;cytoskeletal anchoring at plasma membrane;cell-cell junction assembly;cell-substrate junction assembly;integrin-mediated signaling pathway;viral process;cortical actin cytoskeleton organization;integrin activation;IRE1-mediated unfolded protein response;platelet aggregation
• Cellular component: ruffle;extracellular region;cytosol;cytoskeleton;focal adhesion;cell surface;ruffle membrane;extracellular exosome
• Molecular function: phosphatidylserine binding;integrin binding;structural constituent of cytoskeleton;protein binding;vinculin binding;LIM domain binding;phosphatidylinositol binding;cadherin binding;actin filament binding