LECT2
Basic information
Region (hg38): 5:135922279-135954983
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 LECT2 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 | |||||
| missense | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 1 | 1 |
Variants in LECT2
This is a list of pathogenic ClinVar variants found in the LECT2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-135947338-T-C | not specified | Uncertain significance (Dec 27, 2023) | ||
| 5-135947355-C-T | LECT2-related disorder | Likely benign (Jun 21, 2019) | ||
| 5-135951265-T-C | not specified | Uncertain significance (Dec 13, 2023) | ||
| 5-135951340-T-C | LECT2-related disorder | Benign (Oct 17, 2019) | ||
| 5-135952901-C-T | not specified | Uncertain significance (Mar 31, 2024) | ||
| 5-135952922-T-C | not specified | Uncertain significance (Dec 15, 2022) | ||
| 5-135952944-T-C | not specified | Uncertain significance (Sep 26, 2023) | ||
| 5-135952958-C-T | not specified | Uncertain significance (Sep 07, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LECT2 | protein_coding | protein_coding | ENST00000274507 | 4 | 32756 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00148 | 0.693 | 125680 | 1 | 65 | 125746 | 0.000262 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.0857 | 83 | 85.2 | 0.974 | 0.00000443 | 972 |
| Missense in Polyphen | 36 | 31.745 | 1.134 | 365 | ||
| Synonymous | 0.540 | 27 | 30.8 | 0.876 | 0.00000167 | 297 |
| Loss of Function | 0.748 | 5 | 7.16 | 0.698 | 3.68e-7 | 85 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00175 | 0.00175 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000528 | 0.0000527 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000196 | 0.000196 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Has a neutrophil chemotactic activity. Also a positive regulator of chondrocyte proliferation (PubMed:9524238). Does not show metalloendopeptidase activity (PubMed:27334921). {ECO:0000269|PubMed:27334921, ECO:0000269|PubMed:9524238}.;
- Pathway
- C-MYB transcription factor network
(Consensus)
Recessive Scores
- pRec
- 0.135
Intolerance Scores
- loftool
- 0.769
- rvis_EVS
- 0.44
- rvis_percentile_EVS
- 77.57
Haploinsufficiency Scores
- pHI
- 0.102
- hipred
- N
- hipred_score
- 0.444
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.286
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Lect2
- Phenotype
- immune system phenotype; liver/biliary system phenotype; neoplasm; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cellular phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- skeletal system development;chemotaxis
- Cellular component
- extracellular space;cytoplasm
- Molecular function
- protein binding;identical protein binding;metal ion binding