LIPK
protein-codinglipase family member K, the group of Lipases
Gene summary
Predicted to enable lipase activity. Predicted to be involved in lipid metabolic process. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Jun 2026]
- LIPL2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~46.5 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 LIPK variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001080518.2. 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 | 53 | 6 | 59 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 53 | 6 | 0 | 59 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001073987.1 | 9 | MANE Select | |
| Ensembl | ENSP00000383900.1 | 9 | MANE Select | |
| RefSeq | NP_001365020.1 | 9 | Standard | |
| RefSeq | XP_011538375.1 | 10 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Keratinization
- Developmental Biology
- Formation of the cornified envelope
Biological Process
- lipid catabolic process
- cellular lipid metabolic process
- cornification
Molecular Function
- lipoprotein lipase activity
- lipase activity
Cellular Component
- extracellular region
- intracellular membrane-bounded organelle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000404190
- Coding exons
- 9
- Length
- 28243
- Individuals with no LoFs
- 124603
- Homozygous LoFs
- 5
- Heterozygous LoFs
- 445
- Defined
- 125053
- p
- 0.00180
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.137 | 194 | 199 | 0.973 | 0.00000963 | 2599 |
| Missense (PolyPhen) | 56 | 64.991 | 0.86165 | 926 | ||
| Synonymous | -0.276 | 69 | 66.1 | 1.04 | 0.00000317 | 707 |
| Loss of Function | 1.55 | 12 | 19.4 | 0.619 | 9.68e-7 | 242 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00052 | 0.00052 | rare |
| Latino/Admixed American | 0.00030 | 0.00029 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.0013 | 0.0013 | notable |
| Finnish | 0.011 | 0.011 | notable |
| European (Non-Finnish) | 0.0012 | 0.0012 | notable |
| South Asian | 0.00095 | 0.00092 | rare |
| Other | 0.0015 | 0.0015 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays a highly specific role in the last step of keratinocyte differentiation. May have an essential function in lipid metabolism of the most differentiated epidermal layers. {ECO:0000269|PubMed:17562024}.;
Recessive Scores
- pRec
- 0.0961
Intolerance Scores
- LoFtool
- 0.799
- RVIS EVS
- 0.8
- RVIS percentile EVS
- 87.49
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.165
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |