LCTL
protein-codinglactase like, the group of Glycoside hydrolase family 1
Gene summary
This gene encodes a member of family 1 glycosidases. Glycosidases are enzymes that hydrolyze glycosidic bonds and are classified into families based on primary amino acid sequence. Most members of family 1 have two conserved glutamic acid residues, which are required for enzymatic activity. The mouse ortholog of this protein has been characterized and has a domain structure of an N-terminal signal peptide, glycosidase domain, transmembrane domain, and a short cytoplasmic tail. It lacks one of the conserved glutamic acid residues important for catalysis, and its function remains to be determined (PMID: 12084582). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2013]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~18.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to LCTL variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_207338.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 2 | 3 | 6 | ||
| missense | 106 | 8 | 114 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 107 | 10 | 3 | 120 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_997221.2 | 13 | MANE Select | |
| Ensembl | ENSP00000512002.1 | 13 | MANE Select | |
| RefSeq | NP_001265491.1 | 9 | Standard | |
| RefSeq | NP_001381561.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- carbohydrate metabolic process
Molecular Function
- beta-glucosidase activity
Cellular Component
- endoplasmic reticulum
- endoplasmic reticulum membrane
- brush border
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000341509
- Coding exons
- 13
- Length
- 18801
- Individuals with no LoFs
- 125636
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 111
- Defined
- 125747
- p
- 0.000441
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.881 | 283 | 328 | 0.863 | 0.0000184 | 3716 |
| Missense (PolyPhen) | 122 | 139.53 | 0.87437 | 1564 | ||
| Synonymous | -0.258 | 135 | 131 | 1.03 | 0.00000832 | 1043 |
| Loss of Function | 0.476 | 31 | 34.0 | 0.912 | 0.00000162 | 382 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.00039 | 0.00038 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.0013 | 0.0013 | notable |
| Finnish | 0.00015 | 0.00014 | rare |
| European (Non-Finnish) | 0.00021 | 0.00021 | rare |
| South Asian | 0.0013 | 0.0013 | notable |
| Other | 0.0010 | 0.00098 | notable |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.140
Intolerance Scores
- LoFtool
- 0.919
- RVIS EVS
- 0.09
- RVIS percentile EVS
- 60.68
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.269
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |