LACTB2
protein-codinglactamase beta 2, the group of MBL domain containing glyoxalase 2 subfamily
Gene summary
Enables RNA endonuclease activity; single-stranded RNA binding activity; and zinc ion binding activity. Located in several cellular components, including Golgi apparatus; mitochondrial matrix; and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~33.9 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 LACTB2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_016027.3. 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 | 0 | |||||
| missense | 45 | 4 | 49 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 49 | 4 | 0 | 53 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_057111.1 | 7 | MANE Select | |
| Ensembl | ENSP00000276590.4 | 7 | MANE Select | |
| Ensembl | ENSP00000428801.1 | 7 | Standard | |
| Ensembl | ENSP00000428801.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- RNA phosphodiester bond hydrolysis, endonucleolytic
Molecular Function
- single-stranded RNA binding
- endoribonuclease activity
- protein binding
- zinc ion binding
Cellular Component
- mitochondrial matrix
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000276590
- Coding exons
- 7
- Length
- 33857
- Individuals with no LoFs
- 125716
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 30
- Defined
- 125747
- p
- 0.000123
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.433 | 130 | 145 | 0.899 | 0.00000676 | 1878 |
| Missense (PolyPhen) | 37 | 39.682 | 0.93241 | 497 | ||
| Synonymous | 0.729 | 44 | 50.6 | 0.870 | 0.00000228 | 536 |
| Loss of Function | 1.32 | 9 | 14.4 | 0.624 | 7.56e-7 | 183 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00031 | 0.00031 | rare |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00012 | 0.00012 | rare |
| South Asian | 0.00016 | 0.00013 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Endoribonuclease; cleaves preferentially 3' to purine- pyrimidine dinucleotide motifs in single-stranded RNA. The cleavage product contains a free 3' -OH group. Has no activity with double-stranded RNA or DNA. Required for normal mitochondrial function and cell viability. {ECO:0000269|PubMed:26826708}.;
Recessive Scores
- pRec
- 0.0908
Intolerance Scores
- LoFtool
- 0.655
- RVIS EVS
- -0.27
- RVIS percentile EVS
- 33.97
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.928
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |