TLN2

talin 2, the group of FERM domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 15:62390525-62844631

Links

ENSG00000171914 ∙ NCBI:83660 ∙ OMIM:607349 ∙ HGNC:15447 ∙ Uniprot:Q9Y4G6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• camptodactyly of fingers (Limited), mode of inheritance: AD
• Tourette syndrome (Limited), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TLN2 gene.

• Inborn genetic diseases (98 variants)
• not provided (44 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TLN2 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				19	9	28
missense			101	5	4	110
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding						0
Total	0	0	102	24	13

Variants in TLN2

This is a list of pathogenic ClinVar variants found in the TLN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-62647341-C-T		not specified	Uncertain significance (Jul 25, 2023)
15-62647369-A-G			Uncertain significance (Apr 01, 2019)
15-62647404-C-G		not specified	Uncertain significance (Oct 26, 2022)
15-62652047-C-T		not specified	Uncertain significance (Apr 12, 2023)
15-62653165-T-C		not specified	Uncertain significance (May 05, 2023)
15-62653217-A-C		not specified	Uncertain significance (Feb 11, 2022)
15-62656046-A-T		not specified	Uncertain significance (Dec 28, 2022)
15-62657763-T-C			Benign (Mar 29, 2018)
15-62673877-A-G		not specified	Uncertain significance (Nov 22, 2021)
15-62675229-T-C		not specified	Uncertain significance (Jan 03, 2022)
15-62675268-G-A		not specified	Uncertain significance (May 08, 2023)
15-62675274-C-T		not specified	Uncertain significance (May 03, 2023)
15-62675276-C-T			Likely benign (Feb 01, 2023)
15-62686667-G-C			Likely benign (Dec 31, 2019)
15-62686671-C-T		not specified	Uncertain significance (Oct 14, 2021)
15-62686765-G-T		not specified	Uncertain significance (Feb 11, 2022)
15-62692848-G-A			Likely benign (Jun 11, 2018)
15-62692878-A-C		not specified	Uncertain significance (Dec 07, 2023)
15-62692880-C-G		not specified	Uncertain significance (Aug 04, 2021)
15-62692930-A-G		not specified	Uncertain significance (Sep 17, 2021)
15-62694350-A-G		not specified	Uncertain significance (Feb 13, 2024)
15-62694377-C-G		not specified	Uncertain significance (Jul 05, 2023)
15-62694379-G-A		not specified	Uncertain significance (Dec 14, 2023)
15-62697688-G-C		not specified	Uncertain significance (Sep 29, 2022)
15-62697717-G-A		not specified	Uncertain significance (Aug 03, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TLN2	protein_coding	protein_coding	ENST00000561311	56	454106

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.992	0.00769	125692	0	56	125748	0.000223

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.41	1341	1.49e+3	0.897	0.0000907	16479
Missense in Polyphen		250	352.57	0.70908		3916
Synonymous	-2.28	700	627	1.12	0.0000444	5141
Loss of Function	8.41	26	129	0.201	0.00000651	1501

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000360	0.000360
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.000221	0.000217
Finnish	0.0000949	0.0000924
European (Non-Finnish)	0.000212	0.000211
Middle Eastern	0.000221	0.000217
South Asian	0.000263	0.000261
Other	0.000819	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: As a major component of focal adhesion plaques that links integrin to the actin cytoskeleton, may play an important role in cell adhesion. Recruits PIP5K1C to focal adhesion plaques and strongly activates its kinase activity (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);Focal Adhesion;Integrin (Consensus)

Recessive Scores

• pRec: 0.447

Intolerance Scores

• loftool: 0.525
• rvis_EVS: -3.47
• rvis_percentile_EVS: 0.35

Haploinsufficiency Scores

• pHI: 0.306
• hipred: Y
• hipred_score: 0.637
• ghis: 0.553

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.701

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tln2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms 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); normal phenotype; muscle phenotype; cellular phenotype

Gene ontology

• Biological process: cytoskeletal anchoring at plasma membrane;cell-cell junction assembly;cell adhesion
• Cellular component: ruffle;cytoplasm;plasma membrane;focal adhesion;actin cytoskeleton;synapse
• Molecular function: actin binding;structural molecule activity;structural constituent of cytoskeleton;protein binding;actin filament binding