LZTS2

leucine zipper tumor suppressor 2, the group of Leucine zipper tumor suppressor family

Basic information

Region (hg38): 10:100996618-101007836

Links

ENSG00000107816

∙ NCBI:84445 ∙ OMIM:610454 ∙ HGNC:29381 ∙ Uniprot:Q9BRK4 ∙ 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 LZTS2 gene.

not_specified (131 variants)
not_provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LZTS2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001318100.2. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar	1 clinvar	4
missense			130 clinvar	1 clinvar		131
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	130	4	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LZTS2	protein_coding	protein_coding	ENST00000370220	4	11219

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0461	0.954	125725	0	17	125742	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.735	371	413	0.898	0.0000283	4170
Missense in Polyphen		88	112.11	0.78498		1112
Synonymous	0.264	171	175	0.975	0.0000105	1532
Loss of Function	3.58	8	28.7	0.279	0.00000210	241

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000215	0.000215
Ashkenazi Jewish	0.000107	0.0000992
East Asian	0.0000546	0.0000544
Finnish	0.0000579	0.0000462
European (Non-Finnish)	0.0000840	0.0000703
Middle Eastern	0.0000546	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Negative regulator of katanin-mediated microtubule severing and release from the centrosome. Required for central spindle formation and the completion of cytokinesis. May negatively regulate axonal outgrowth by preventing the formation of microtubule bundles that are necessary for transport within the elongating axon. Negative regulator of the Wnt signaling pathway. Represses beta-catenin-mediated transcriptional activation by promoting the nuclear exclusion of beta-catenin. {ECO:0000255|HAMAP-Rule:MF_03026, ECO:0000269|PubMed:17000760, ECO:0000269|PubMed:17351128, ECO:0000269|PubMed:17950943, ECO:0000269|PubMed:18490357}.;

Recessive Scores

pRec: 0.112

Intolerance Scores

loftool: 0.569
rvis_EVS: -1.2
rvis_percentile_EVS: 5.83

Haploinsufficiency Scores

pHI: 0.178
hipred: Y
hipred_score: 0.518
ghis: 0.620

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Lzts2
Phenotype: endocrine/exocrine gland phenotype; renal/urinary system phenotype; embryo phenotype; reproductive system phenotype;

Zebrafish Information Network

Gene name: lzts2a
Affected structure: head
Phenotype tag: abnormal
Phenotype quality: decreased size

Gene ontology

Biological process: mitotic cytokinesis;kidney development;negative regulation of cell population proliferation;Wnt signaling pathway;microtubule severing;nuclear export;spindle midzone assembly;negative regulation of canonical Wnt signaling pathway;negative regulation of protein localization to nucleus
Cellular component: centrosome;cytosol;microtubule;plasma membrane;midbody;vesicle
Molecular function: protein binding