PIP4P2
protein-codingphosphatidylinositol-4,5-bisphosphate 4-phosphatase 2, the group of Phosphoinositide phosphatases
Gene summary
TMEM55A catalyzes the degradation of phosphatidylinositol 4,5-bisphosphate (PtdIns-4,5-P2) by removing the 4-phosphate (Ungewickell et al., 2005 [PubMed 16365287]).[supplied by OMIM, Mar 2008]
- TMEM55A
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~47.1 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 PIP4P2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_018710.3. 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 | 36 | 36 | ||||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 41 | 0 | 0 | 41 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_061180.1 | 7 | MANE Select | |
| Ensembl | ENSP00000285419.3 | 7 | MANE Select | |
| Ensembl | ENSP00000429280.1 | 5 | Standard | |
| Ensembl | ENSP00000429112.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Phosphatidylinositol signaling system - Homo sapiens (human)
- 3-phosphoinositide degradation
- D-<i>myo</i>-inositol-5-phosphate metabolism
- superpathway of inositol phosphate compounds
Biological Process
- phosphatidylinositol dephosphorylation
Molecular Function
- phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity
Cellular Component
- lysosomal membrane
- integral component of membrane
- late endosome membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000285419
- Coding exons
- 7
- Length
- 47269
- Individuals with no LoFs
- 125734
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 14
- Defined
- 125748
- p
- 0.0000557
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.21 | 106 | 147 | 0.720 | 0.00000768 | 1638 |
| Missense (PolyPhen) | 51 | 78.628 | 0.64862 | 918 | ||
| Synonymous | 1.03 | 41 | 50.3 | 0.816 | 0.00000234 | 527 |
| Loss of Function | 1.88 | 8 | 16.1 | 0.496 | 0.00000109 | 162 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000031 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000055 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000089 | 0.000088 | rare |
| South Asian | 0.000034 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate. Does not hydrolyze phosphatidylinositol 3,4,5-trisphosphate, phosphatidylinositol 3,4-bisphosphate, inositol 3,5-bisphosphate, inositol 3,4- bisphosphate, phosphatidylinositol 5-monophosphate, phosphatidylinositol 4-monophosphate and phosphatidylinositol 3- monophosphate. {ECO:0000269|PubMed:16365287}.;
Recessive Scores
- pRec
- 0.126
Intolerance Scores
- RVIS EVS
- 0.04
- RVIS percentile EVS
- 56.64
Essentials
- Essential (gene trap)
- N