LATS1
large tumor suppressor kinase 1, the group of AGC family kinases
Basic information
Region (hg38): 6:149658153-149718105
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LATS1 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 | 1 | |||||
| missense | 34 | 37 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 34 | 3 | 1 |
Variants in LATS1
This is a list of pathogenic ClinVar variants found in the LATS1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-149661790-G-A | not specified | Uncertain significance (May 01, 2024) | ||
| 6-149662082-C-T | not specified | Uncertain significance (Jan 08, 2024) | ||
| 6-149676638-G-A | not specified | Uncertain significance (Feb 14, 2023) | ||
| 6-149676695-C-T | Malignant peritoneal mesothelioma | Likely pathogenic (Feb 18, 2019) | ||
| 6-149676701-T-C | not specified | Uncertain significance (Apr 26, 2023) | ||
| 6-149676726-G-A | not specified | Uncertain significance (Sep 25, 2023) | ||
| 6-149679896-C-T | not specified | Uncertain significance (May 07, 2024) | ||
| 6-149679921-G-A | Likely benign (Apr 01, 2023) | |||
| 6-149679992-G-T | not specified | Uncertain significance (Apr 04, 2023) | ||
| 6-149680019-C-T | Multiple myeloma | Likely pathogenic (Aug 31, 2019) | ||
| 6-149680103-C-G | Ependymoma | Uncertain significance (Dec 29, 2017) | ||
| 6-149680331-T-C | not specified | Uncertain significance (May 09, 2022) | ||
| 6-149680439-C-A | Teratoma | Uncertain significance (Jan 01, 2023) | ||
| 6-149683152-T-C | not specified | Uncertain significance (Jan 03, 2024) | ||
| 6-149683201-G-A | not specified | Uncertain significance (Mar 01, 2024) | ||
| 6-149683278-T-C | not specified | Uncertain significance (Aug 13, 2021) | ||
| 6-149683408-T-C | not specified | Uncertain significance (Nov 12, 2021) | ||
| 6-149683420-G-A | not specified | Uncertain significance (Feb 10, 2023) | ||
| 6-149683432-G-C | not specified | Uncertain significance (Dec 16, 2023) | ||
| 6-149683498-G-A | Likely benign (Apr 30, 2018) | |||
| 6-149683546-T-C | not specified | Uncertain significance (Jul 12, 2023) | ||
| 6-149683584-C-T | not specified | Uncertain significance (Jun 28, 2022) | ||
| 6-149683630-T-G | not specified | Uncertain significance (Apr 20, 2024) | ||
| 6-149683741-C-T | not specified | Uncertain significance (Apr 23, 2024) | ||
| 6-149683755-G-C | not specified | Uncertain significance (May 10, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LATS1 | protein_coding | protein_coding | ENST00000543571 | 7 | 60104 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.000131 | 125730 | 0 | 17 | 125747 | 0.0000676 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.31 | 454 | 615 | 0.738 | 0.0000321 | 7466 |
| Missense in Polyphen | 144 | 264.14 | 0.54517 | 3095 | ||
| Synonymous | 0.104 | 202 | 204 | 0.991 | 0.0000103 | 2182 |
| Loss of Function | 5.90 | 6 | 51.9 | 0.116 | 0.00000335 | 524 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000176 | 0.000176 |
| Ashkenazi Jewish | 0.0000993 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000880 | 0.0000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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 LATS1 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 maintenance of ploidy through its actions in both mitotic progression and the G1 tetraploidy checkpoint. Negatively regulates G2/M transition by down-regulating CDK1 kinase activity. Involved in the control of p53 expression. Affects cytokinesis by regulating actin polymerization through negative modulation of LIMK1. May also play a role in endocrine function. Plays a role in mammary gland epithelial cells differentiation, both through the Hippo signaling pathway and the intracellular estrogen receptor signaling pathway by promoting the degradation of ESR1 (PubMed:28068668). {ECO:0000269|PubMed:10518011, ECO:0000269|PubMed:10831611, ECO:0000269|PubMed:15122335, ECO:0000269|PubMed:15220930, ECO:0000269|PubMed:18158288, ECO:0000269|PubMed:19927127, ECO:0000269|PubMed:28068668}.;
- Pathway
- Hippo signaling pathway - Homo sapiens (human);Hippo signaling pathway - multiple species - Homo sapiens (human);Mesodermal Commitment Pathway;Signal Transduction;Signaling by Hippo
(Consensus)
Recessive Scores
- pRec
- 0.585
Intolerance Scores
- loftool
- 0.250
- rvis_EVS
- -0.02
- rvis_percentile_EVS
- 52.28
Haploinsufficiency Scores
- pHI
- 0.322
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.557
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.954
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Lats1
- 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); neoplasm; normal 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); reproductive system 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); liver/biliary system phenotype; cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- lats1
- Affected structure
- convergent extension involved in gastrulation
- Phenotype tag
- abnormal
- Phenotype quality
- disrupted
Gene ontology
- Biological process
- G1/S transition of mitotic cell cycle;G2/M transition of mitotic cell cycle;sister chromatid segregation;inner cell mass cell fate commitment;inner cell mass cellular morphogenesis;protein phosphorylation;hormone-mediated signaling pathway;peptidyl-serine phosphorylation;keratinocyte differentiation;regulation of actin filament polymerization;positive regulation of peptidyl-serine phosphorylation;regulation of intracellular estrogen receptor signaling pathway;cellular protein localization;hippo signaling;intracellular signal transduction;positive regulation of apoptotic process;regulation of protein complex assembly;negative regulation of cyclin-dependent protein serine/threonine kinase activity;regulation of organ growth;cytoplasmic sequestering of protein;cell division;mammary gland epithelial cell differentiation;negative regulation of canonical Wnt signaling pathway;regulation of ubiquitin-dependent protein catabolic process
- Cellular component
- spindle pole;microtubule organizing center;cytosol
- Molecular function
- magnesium ion binding;protein serine/threonine kinase activity;protein binding;ATP binding;protein kinase binding;estrogen receptor binding