LACRT
Basic information
Region (hg38): 12:54630810-54634895
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 LACRT 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 | 0 | |||||
| missense | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 0 | 0 |
Variants in LACRT
This is a list of pathogenic ClinVar variants found in the LACRT region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-54631759-C-G | not specified | Uncertain significance (Feb 28, 2024) | ||
| 12-54631775-C-A | not specified | Uncertain significance (May 18, 2022) | ||
| 12-54631776-A-C | not specified | Uncertain significance (Apr 12, 2024) | ||
| 12-54631814-T-A | not specified | Uncertain significance (Mar 20, 2024) | ||
| 12-54631828-C-T | not specified | Uncertain significance (Sep 13, 2023) | ||
| 12-54632270-G-A | not specified | Uncertain significance (Mar 22, 2023) | ||
| 12-54632303-G-A | not specified | Uncertain significance (Oct 05, 2023) | ||
| 12-54632334-G-C | not specified | Uncertain significance (Apr 08, 2024) | ||
| 12-54633191-T-C | not specified | Uncertain significance (Feb 23, 2023) | ||
| 12-54634799-C-A | not specified | Uncertain significance (Nov 09, 2021) | ||
| 12-54634811-C-T | not specified | Uncertain significance (Dec 16, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LACRT | protein_coding | protein_coding | ENST00000257867 | 5 | 4085 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000119 | 0.398 | 125692 | 1 | 42 | 125735 | 0.000171 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.367 | 82 | 73.2 | 1.12 | 0.00000357 | 870 |
| Missense in Polyphen | 7 | 6.8164 | 1.0269 | 57 | ||
| Synonymous | 0.399 | 28 | 30.8 | 0.909 | 0.00000181 | 288 |
| Loss of Function | 0.111 | 6 | 6.30 | 0.952 | 2.65e-7 | 81 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000268 | 0.000268 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000163 | 0.000163 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000705 | 0.0000703 |
| Middle Eastern | 0.000163 | 0.000163 |
| South Asian | 0.000752 | 0.000719 |
| Other | 0.000490 | 0.000489 |
dbNSFP
Source:
- Function
- FUNCTION: Modulates secretion by lacrimal acinar cells.;
Recessive Scores
- pRec
- 0.0800
Intolerance Scores
- loftool
- 0.591
- rvis_EVS
- -0.14
- rvis_percentile_EVS
- 42.88
Haploinsufficiency Scores
- pHI
- 0.0721
- hipred
- N
- hipred_score
- 0.146
- ghis
- 0.440
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.601
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Medium |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- protein acetylation;positive regulation of cell population proliferation;regulation of signaling receptor activity;epithelial structure maintenance;positive regulation of macroautophagy;calcium-mediated signaling;negative regulation of lipopolysaccharide-mediated signaling pathway;calcineurin-NFAT signaling cascade;protein localization to Golgi apparatus;defense response to bacterium;negative regulation of apoptotic process;positive regulation of epithelial cell proliferation;positive regulation of peptidyl-tyrosine phosphorylation;positive regulation of calcium-mediated signaling;positive regulation of secretion;positive regulation of release of sequestered calcium ion into cytosol;positive regulation of epithelial cell proliferation involved in wound healing;tear secretion;positive regulation of calcineurin-NFAT signaling cascade
- Cellular component
- extracellular region;extracellular space;secretory granule
- Molecular function
- fibronectin binding;protein binding;collagen binding;growth factor activity;laminin-1 binding;protein N-terminus binding