PLPPR5
protein-codingphospholipid phosphatase related 5, the group of Phospholipid phosphatase related
Gene summary
The protein encoded by this gene is a type 2 member of the phosphatidic acid phosphatase (PAP) family. All type 2 members of this protein family contain 6 transmembrane regions, and a consensus N-glycosylation site. PAPs convert phosphatidic acid to diacylglycerol, and function in de novo synthesis of glycerolipids as well as in receptor-activated signal transduction mediated by phospholipase D. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [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 ~337.7 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 PLPPR5 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001037317.2. 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 | 32 | 32 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 32 | 0 | 0 | 32 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001032394.1 | 6 | MANE Select | |
| Ensembl | ENSP00000263177.4 | 6 | MANE Select | |
| RefSeq | NP_001010861.1 | 6 | Standard | |
| Ensembl | ENSP00000359207.3 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Signaling by GPCR
- Signal Transduction
- Lysosphingolipid and LPA receptors
- Class A/1 (Rhodopsin-like receptors)
- GPCR ligand binding
Biological Process
- phospholipid metabolic process
- positive regulation of neuron projection development
- phospholipid dephosphorylation
- positive regulation of filopodium assembly
Molecular Function
- phosphatidate phosphatase activity
- phosphatase activity
- lipid phosphatase activity
Cellular Component
- plasma membrane
- integral component of plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000263177
- Coding exons
- 6
- Length
- 114783
- Individuals with no LoFs
- 125709
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 7
- Defined
- 125716
- p
- 0.0000278
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.47 | 126 | 182 | 0.693 | 0.00000857 | 2084 |
| Missense (PolyPhen) | 30 | 71.813 | 0.41775 | 827 | ||
| Synonymous | -2.27 | 92 | 68.2 | 1.35 | 0.00000326 | 646 |
| Loss of Function | 2.58 | 5 | 16.2 | 0.308 | 0.00000115 | 158 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0.00011 | 0.000099 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000036 | 0.000035 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Induces filopodia formation and promotes neurite growth in a CDC42-independent manner; impedes neurite growth inhibitory- mediated axonal retraction. {ECO:0000250|UniProtKB:Q8BJ52}.;
Intolerance Scores
- RVIS EVS
- -0.38
- RVIS percentile EVS
- 27.42
Essentials
- Essential (gene trap)
- N