LMF2
protein-codinglipase maturation factor 2
Gene summary
Predicted to be involved in protein maturation. Located in membrane. [provided by Alliance of Genome Resources, Jul 2025]
- TMEM153
- TMEM112B
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~4.8 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 LMF2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_033200.3. 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 | 3 | 4 | 7 | |||
| missense | 191 | 11 | 202 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 201 | 15 | 0 | 216 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_149977.2 | 14 | MANE Select | |
| Ensembl | ENSP00000424381.1 | 14 | MANE Select | |
| RefSeq | NP_001350745.1 | 13 | Standard | |
| Ensembl | ENSP00000216080.5 | 13 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| lmf2b | Danio rerio | Structure: blood circulation Quality: disrupted abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Transport of small molecules
- Assembly of active LPL and LIPC lipase complexes
- Plasma lipoprotein assembly, remodeling, and clearance
- Plasma lipoprotein remodeling
Biological Process
- protein maturation
Molecular Function
- protein binding
Cellular Component
- endoplasmic reticulum membrane
- membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000474879
- Coding exons
- 14
- Length
- 4760
- Individuals with no LoFs
- 125500
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 167
- Defined
- 125668
- p
- 0.000669
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -2.52 | 577 | 430 | 1.34 | 0.0000284 | 4374 |
| Missense (PolyPhen) | 217 | 174.78 | 1.2416 | 1817 | ||
| Synonymous | -7.08 | 324 | 197 | 1.64 | 0.0000130 | 1547 |
| Loss of Function | -3.80 | 61 | 36.3 | 1.68 | 0.00000181 | 336 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0033 | 0.0031 | notable |
| Latino/Admixed American | 0.00070 | 0.00069 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.0011 | 0.0011 | notable |
| Finnish | 0.00013 | 0.000092 | rare |
| European (Non-Finnish) | 0.00029 | 0.00027 | rare |
| South Asian | 0.0013 | 0.0013 | notable |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in the maturation of specific proteins in the endoplasmic reticulum. May be required for maturation and transport of active lipoprotein lipase (LPL) through the secretory pathway (By similarity). {ECO:0000250}.;
Intolerance Scores
- LoFtool
- 0.887
- RVIS EVS
- -1.29
- RVIS percentile EVS
- 5
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.167
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |