LZTS2

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

Basic information

Region (hg38): 10:100996617-101007836

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.

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.

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	1	2
missense			56			56
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	56	1	1

Variants in LZTS2

This is a list of pathogenic ClinVar variants found in the LZTS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-101002563-G-A		not specified	Uncertain significance (Oct 05, 2023)
10-101002566-C-G		not specified	Uncertain significance (Dec 19, 2023)
10-101002656-G-A		not specified	Uncertain significance (Oct 12, 2022)
10-101002671-C-G		not specified	Uncertain significance (May 04, 2023)
10-101002682-C-T			Benign (Apr 30, 2018)
10-101002729-G-A		not specified	Uncertain significance (Sep 21, 2023)
10-101002753-C-T		not specified	Uncertain significance (Jun 11, 2024)
10-101002813-A-G		not specified	Uncertain significance (Mar 30, 2022)
10-101002864-A-G		not specified	Uncertain significance (Jul 26, 2022)
10-101002878-C-T		not specified	Uncertain significance (Jun 22, 2023)
10-101002879-G-A		not specified	Uncertain significance (Jun 17, 2024)
10-101002890-G-T		not specified	Uncertain significance (May 13, 2024)
10-101002894-A-G		not specified	Uncertain significance (Dec 12, 2023)
10-101002900-G-A		not specified	Uncertain significance (May 31, 2023)
10-101002920-A-C			Likely benign (-)
10-101003515-G-C		not specified	Uncertain significance (Jul 13, 2022)
10-101003518-G-C		not specified	Uncertain significance (May 11, 2022)
10-101003609-G-A		not specified	Uncertain significance (May 30, 2024)
10-101003637-C-T		not specified	Uncertain significance (Dec 11, 2023)
10-101003745-C-T		not specified	Uncertain significance (Mar 07, 2024)
10-101003864-G-A		not specified	Uncertain significance (May 09, 2023)
10-101003895-C-T		not specified	Uncertain significance (Feb 27, 2023)
10-101003993-C-T		not specified	Uncertain significance (Sep 16, 2021)
10-101004038-C-T		not specified	Uncertain significance (Nov 09, 2023)
10-101004104-C-T		not specified	Uncertain significance (Nov 18, 2022)

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