LYPLA2
protein-codinglysophospholipase 2, the group of Depalmitoylases
Gene summary
Lysophospholipases are enzymes that act on biological membranes to regulate the multifunctional lysophospholipids. There are alternatively spliced transcript variants described for this gene but the full length nature is not known yet. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~4.4 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 LYPLA2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_007260.3. 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 | 27 | 27 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 29 | 0 | 0 | 29 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_009191.1 | 9 | MANE Select | |
| Ensembl | ENSP00000363638.3 | 9 | MANE Select | |
| Ensembl | ENSP00000363625.1 | 6 | Standard | |
| Ensembl | ENSP00000363625.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Glycerophospholipid metabolism - Homo sapiens (human)
- Developmental Biology
- L1CAM interactions
- Axon guidance
Biological Process
- protein depalmitoylation
- fatty acid metabolic process
- axon guidance
Molecular Function
- palmitoyl-(protein) hydrolase activity
- cadherin binding
- carboxylic ester hydrolase activity
Cellular Component
- cytoplasm
- Golgi stack
- cytosol
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000374514
- Coding exons
- 9
- Length
- 4570
- Individuals with no LoFs
- 125735
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 4
- Defined
- 125739
- p
- 0.0000159
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.70 | 88 | 146 | 0.604 | 0.00000860 | 1489 |
| Missense (PolyPhen) | 20 | 47.233 | 0.42343 | 552 | ||
| Synonymous | -0.310 | 62 | 59.0 | 1.05 | 0.00000376 | 479 |
| Loss of Function | 3.19 | 1 | 13.8 | 0.0724 | 7.52e-7 | 141 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Hydrolyzes fatty acids from S-acylated cysteine residues in proteins such as trimeric G alpha proteins, GAP43, ZDHHC6 or HRAS (PubMed:21152083, PubMed:28826475). Deacylates GAP43 (PubMed:21152083). Mediates depalmitoylation of ZDHHC6 (PubMed:28826475). Has lysophospholipase activity (By similarity). {ECO:0000250|UniProtKB:Q9WTL7, ECO:0000269|PubMed:21152083, ECO:0000269|PubMed:28826475}.;
Recessive Scores
- pRec
- 0.100
Intolerance Scores
- LoFtool
- 0.0699
- RVIS EVS
- -0.3
- RVIS percentile EVS
- 32.62
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.925
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Medium |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |