LZTS1

leucine zipper tumor suppressor 1, the group of Leucine zipper tumor suppressor family

Basic information

Region (hg38): 8:20246165-20303963

Links

ENSG00000061337 ∙ NCBI:11178 ∙ OMIM:606551 ∙ HGNC:13861 ∙ Uniprot:Q9Y250 ∙ 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 LZTS1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LZTS1 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				81	9	90
missense			154	14	6	174
nonsense			1			1
start loss						0
frameshift			2			2
inframe indel			6			6
splice donor/acceptor (+/-2bp)						0
splice region			1	4	1	6
non coding				8	9	17
Total	0	0	163	103	24

Variants in LZTS1

This is a list of pathogenic ClinVar variants found in the LZTS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-20249712-A-T		LZTS1-related disorder	Benign (Nov 06, 2019)
8-20249727-T-A			Uncertain significance (Apr 06, 2023)
8-20249749-G-A		not specified	Likely benign (Mar 19, 2024)
8-20249758-G-A			Likely benign (Jul 06, 2022)
8-20249763-C-T		not specified	Conflicting classifications of pathogenicity (Oct 12, 2024)
8-20249764-C-A			Likely benign (Mar 10, 2023)
8-20249772-G-C			Uncertain significance (Mar 23, 2023)
8-20249784-A-G			Likely benign (Oct 27, 2022)
8-20249790-C-G			Uncertain significance (Jun 25, 2022)
8-20249794-G-A			Likely benign (May 11, 2022)
8-20249796-C-T		not specified	Uncertain significance (Oct 26, 2023)
8-20249797-G-A			Likely benign (Oct 27, 2022)
8-20249807-C-T			Uncertain significance (Mar 03, 2023)
8-20249808-G-A			Uncertain significance (Nov 18, 2023)
8-20249811-C-G			Uncertain significance (Nov 19, 2023)
8-20249814-G-C			Benign (Jan 26, 2024)
8-20249820-G-C			Uncertain significance (Jun 13, 2023)
8-20249833-C-T			Benign (Oct 23, 2023)
8-20249837-C-T			Uncertain significance (Dec 22, 2022)
8-20249838-G-A		LZTS1-related disorder • not specified	Uncertain significance (Mar 20, 2023)
8-20249845-C-G			Likely benign (Jun 21, 2022)
8-20249846-C-T			Uncertain significance (Aug 31, 2022)
8-20249847-G-A			Uncertain significance (Jul 25, 2023)
8-20249862-C-T			Uncertain significance (Jan 29, 2024)
8-20249863-G-A			Likely benign (Jul 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LZTS1	protein_coding	protein_coding	ENST00000381569	3	57799

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.955	0.0451	125740	0	6	125746	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.217	359	371	0.968	0.0000256	3831
Missense in Polyphen		119	136.68	0.87064		1502
Synonymous	0.100	174	176	0.990	0.0000125	1217
Loss of Function	3.56	2	18.5	0.108	7.99e-7	225

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000580	0.0000580
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000549	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000184	0.0000176
Middle Eastern	0.0000549	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the regulation of cell growth. May stabilize the active CDC2-cyclin B1 complex and thereby contribute to the regulation of the cell cycle and the prevention of uncontrolled cell proliferation. May act as a tumor suppressor. {ECO:0000269|PubMed:10097140, ECO:0000269|PubMed:11464283, ECO:0000269|PubMed:11504921}.
• Disease: DISEASE: Esophageal cancer (ESCR) [MIM:133239]: A malignancy of the esophagus. The most common types are esophageal squamous cell carcinoma and adenocarcinoma. Cancer of the esophagus remains a devastating disease because it is usually not detected until it has progressed to an advanced incurable stage. {ECO:0000269|PubMed:10097140}. Note=The disease may be caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.219

Intolerance Scores

• loftool: 0.118
• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.49

Haploinsufficiency Scores

• pHI: 0.211
• hipred: Y
• hipred_score: 0.707
• ghis: 0.575

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.907

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lzts1
• Phenotype: cellular 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; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: transcription, DNA-templated;regulation of transcription, DNA-templated;negative regulation of macroautophagy;mitotic cell cycle phase transition
• Cellular component: cytoplasm;postsynaptic density;cell junction;dendritic spine;postsynaptic membrane
• Molecular function: DNA binding;DNA-binding transcription factor activity;protein binding;microtubule binding