PIP4P1
protein-codingphosphatidylinositol-4,5-bisphosphate 4-phosphatase 1, the group of Phosphoinositide phosphatases
Gene summary
TMEM55B 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]
- C14orf9
- TMEM55B
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~3.8 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 PIP4P1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_144568.4. 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 | 2 | 1 | 3 | |||
| missense | 29 | 29 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 32 | 0 | 1 | 33 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_653169.2 | 7 | MANE Select | |
| Ensembl | ENSP00000250489.4 | 7 | MANE Select | |
| RefSeq | NP_001094284.1 | 7 | Standard | |
| Ensembl | ENSP00000381102.4 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Phosphatidylinositol signaling system - Homo sapiens (human)
- Gene expression (Transcription)
- Synthesis of PIPs in the nucleus
- Generic Transcription Pathway
- Metabolism of lipids
Biological Process
- phospholipid metabolic process
- phosphatidylinositol dephosphorylation
Molecular Function
- phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity
Cellular Component
- nucleoplasm
- lysosomal membrane
- integral component of membrane
- late endosome membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000398020
- Coding exons
- 7
- Length
- 3894
- Individuals with no LoFs
- 125744
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 4
- Defined
- 125748
- p
- 0.0000159
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.54 | 96 | 149 | 0.644 | 0.00000822 | 1798 |
| Missense (PolyPhen) | 28 | 57.39 | 0.48789 | 657 | ||
| Synonymous | 0.601 | 47 | 52.5 | 0.895 | 0.00000247 | 598 |
| Loss of Function | 3.19 | 2 | 15.6 | 0.128 | 0.00000103 | 166 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000027 | 0.000018 | rare |
| South Asian | 0 | 0.0 | absent |
| 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
- 0.130
Intolerance Scores
- RVIS EVS
- -0.27
- RVIS percentile EVS
- 33.97
Essentials
- Essential (gene trap)
- N