LZTS2

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

Basic information

Region (hg38): 10:100996618-101007836

Links

ENSG00000107816NCBI:84445OMIM:610454HGNC:29381Uniprot:Q9BRK4AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
1
clinvar
2
missense
56
clinvar
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)3121801
10-101002566-C-G not specified Uncertain significance (Dec 19, 2023)3121802
10-101002656-G-A not specified Uncertain significance (Oct 12, 2022)2370647
10-101002671-C-G not specified Uncertain significance (May 04, 2023)2510700
10-101002682-C-T Benign (Apr 30, 2018)736827
10-101002729-G-A not specified Uncertain significance (Sep 21, 2023)3121800
10-101002753-C-T not specified Uncertain significance (Jun 11, 2024)3292443
10-101002813-A-G not specified Uncertain significance (Mar 30, 2022)2280943
10-101002864-A-G not specified Uncertain significance (Jul 26, 2022)2215205
10-101002878-C-T not specified Uncertain significance (Jun 22, 2023)2600140
10-101002879-G-A not specified Uncertain significance (Jun 17, 2024)3292441
10-101002890-G-T not specified Uncertain significance (May 13, 2024)3292442
10-101002894-A-G not specified Uncertain significance (Dec 12, 2023)3121803
10-101002900-G-A not specified Uncertain significance (May 31, 2023)2540390
10-101002920-A-C Likely benign (-)1206247
10-101003515-G-C not specified Uncertain significance (Jul 13, 2022)2301771
10-101003518-G-C not specified Uncertain significance (May 11, 2022)2406956
10-101003609-G-A not specified Uncertain significance (May 30, 2024)3292440
10-101003637-C-T not specified Uncertain significance (Dec 11, 2023)3121804
10-101003745-C-T not specified Uncertain significance (Mar 07, 2024)3121805
10-101003864-G-A not specified Uncertain significance (May 09, 2023)2509070
10-101003895-C-T not specified Uncertain significance (Feb 27, 2023)2463029
10-101003993-C-T not specified Uncertain significance (Sep 16, 2021)2250042
10-101004038-C-T not specified Uncertain significance (Nov 09, 2023)3121806
10-101004104-C-T not specified Uncertain significance (Nov 18, 2022)2327620

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
LZTS2protein_codingprotein_codingENST00000370220 411219
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.04610.9541257250171257420.0000676
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7353714130.8980.00002834170
Missense in Polyphen88112.110.784981112
Synonymous0.2641711750.9750.00001051532
Loss of Function3.58828.70.2790.00000210241

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002150.000215
Ashkenazi Jewish0.0001070.0000992
East Asian0.00005460.0000544
Finnish0.00005790.0000462
European (Non-Finnish)0.00008400.0000703
Middle Eastern0.00005460.0000544
South Asian0.00003270.0000327
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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