LZTS2
Basic information
Region (hg38): 10:100996618-101007836
Links
Phenotypes
GenCC
Source:
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 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 | 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:
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:
- 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