LATS2

large tumor suppressor kinase 2, the group of AGC family kinases

Basic information

Region (hg38): 13:20973036-21061586

Links

ENSG00000150457 ∙ NCBI:26524 ∙ OMIM:604861 ∙ HGNC:6515 ∙ Uniprot:Q9NRM7 ∙ 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 LATS2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LATS2 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	8	13
missense			48	2	3	53
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	48	7	12

Variants in LATS2

This is a list of pathogenic ClinVar variants found in the LATS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-20974885-C-G		not specified	Uncertain significance (Feb 21, 2024)
13-20974900-C-T			Likely benign (Dec 11, 2018)
13-20974916-G-C		not specified	Uncertain significance (Oct 05, 2022)
13-20974976-C-T		not specified	Uncertain significance (Nov 08, 2022)
13-20975032-G-A			Likely benign (Jun 01, 2020)
13-20975040-G-A		not specified	Uncertain significance (Feb 12, 2024)
13-20975052-T-A		not specified	Uncertain significance (May 30, 2024)
13-20975100-C-T			Benign (Jul 13, 2018)
13-20975109-G-A		not specified	Uncertain significance (Sep 22, 2023)
13-20975148-T-C		not specified	Uncertain significance (Mar 07, 2024)
13-20975169-C-T		not specified	Uncertain significance (Dec 13, 2021)
13-20975201-G-A		not specified	Uncertain significance (Dec 27, 2023)
13-20975215-G-A			Benign (Jul 15, 2018)
13-20975345-G-A		not specified	Uncertain significance (Jun 04, 2024)
13-20975348-T-C			Likely benign (Jun 01, 2018)
13-20979717-G-A		not specified	Uncertain significance (Dec 01, 2022)
13-20979763-T-TG		Malignant peritoneal mesothelioma	Likely pathogenic (Feb 18, 2019)
13-20981461-T-C			Benign (Dec 31, 2019)
13-20981470-G-A			Benign (Dec 31, 2019)
13-20981471-C-T		not specified	Uncertain significance (Feb 15, 2023)
13-20981575-G-C			Benign (Jul 13, 2018)
13-20981585-C-T		not specified	Uncertain significance (Apr 10, 2023)
13-20981586-G-A		not specified	Uncertain significance (May 08, 2023)
13-20981592-T-G		not specified	Uncertain significance (Sep 20, 2023)
13-20983240-G-C			Benign (Feb 26, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LATS2	protein_coding	protein_coding	ENST00000382592	7	88516

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.988	0.0119	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.21	499	659	0.757	0.0000438	7032
Missense in Polyphen		176	294.52	0.59758		3296
Synonymous	0.858	284	303	0.937	0.0000234	2188
Loss of Function	4.74	5	35.4	0.141	0.00000178	397

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000123
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.000185	0.000185
European (Non-Finnish)	0.0000272	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negative regulator of YAP1 in the Hippo signaling pathway that plays a pivotal role in organ size control and tumor suppression by restricting proliferation and promoting apoptosis. The core of this pathway is composed of a kinase cascade wherein STK3/MST2 and STK4/MST1, in complex with its regulatory protein SAV1, phosphorylates and activates LATS1/2 in complex with its regulatory protein MOB1, which in turn phosphorylates and inactivates YAP1 oncoprotein and WWTR1/TAZ. Phosphorylation of YAP1 by LATS2 inhibits its translocation into the nucleus to regulate cellular genes important for cell proliferation, cell death, and cell migration. Acts as a tumor suppressor which plays a critical role in centrosome duplication, maintenance of mitotic fidelity and genomic stability. Negatively regulates G1/S transition by down-regulating cyclin E/CDK2 kinase activity. Negative regulator of the androgen receptor. Phosphorylates SNAI1 in the nucleus leading to its nuclear retention and stabilization, which enhances its epithelial-mesenchymal transition and tumor cell invasion/migration activities. This tumor-promoting activity is independent of its effects upon YAP1 or WWTR1/TAZ. {ECO:0000269|PubMed:10871863, ECO:0000269|PubMed:12853976, ECO:0000269|PubMed:15131260, ECO:0000269|PubMed:18158288, ECO:0000269|PubMed:21952048}.
• Pathway: Hippo signaling pathway - Homo sapiens (human);Hippo signaling pathway - multiple species - Homo sapiens (human);EMT transition in Colorectal Cancer;Signal Transduction;Coregulation of Androgen receptor activity;Signaling by Hippo (Consensus)

Recessive Scores

• pRec: 0.328

Intolerance Scores

• loftool: 0.260
• rvis_EVS: 0.36
• rvis_percentile_EVS: 74.71

Haploinsufficiency Scores

• pHI: 0.326
• hipred: Y
• hipred_score: 0.792
• ghis: 0.523

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.387

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lats2
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype; muscle phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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); 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; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; embryo phenotype

Zebrafish Information Network

• Gene name: lats2
• Affected structure: convergent extension involved in gastrulation
• Phenotype tag: abnormal
• Phenotype quality: disrupted

Gene ontology

• Biological process: G1/S transition of mitotic cell cycle;protein phosphorylation;hormone-mediated signaling pathway;peptidyl-serine phosphorylation;hippo signaling;intracellular signal transduction;positive regulation of apoptotic process;negative regulation of cyclin-dependent protein serine/threonine kinase activity;regulation of organ growth;cell division;negative regulation of canonical Wnt signaling pathway
• Cellular component: spindle pole;nucleus;microtubule organizing center;cytosol
• Molecular function: protein serine/threonine kinase activity;protein binding;ATP binding;metal ion binding