PDXP
protein-codingpyridoxal phosphatase, the group of HAD Asp-based protein phosphatases
Gene summary
Pyridoxal 5-prime-phosphate (PLP) is the active form of vitamin B6 that acts as a coenzyme in maintaining biochemical homeostasis. The preferred degradation route from PLP to 4-pyridoxic acid involves the dephosphorylation of PLP by PDXP (Jang et al., 2003 [PubMed 14522954]).[supplied by OMIM, Mar 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~8.2 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 PDXP variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_020315.5. 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 | 2 | ||||
| missense | 44 | 1 | 45 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 44 | 3 | 0 | 47 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_064711.1 | 2 | MANE Select | |
| Ensembl | ENSP00000215904.6 | 2 | MANE Select | |
| Ensembl | ENSP00000385336.1 | 1 | Standard | |
| Ensembl | ENSP00000385336.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Vitamin B6 metabolism - Homo sapiens (human)
- Hypophosphatasia
- Vitamin B6 Metabolism
- pyridoxal 5,-phosphate salvage
Biological Process
- protein dephosphorylation
- regulation of mitotic nuclear division
- dephosphorylation
- positive regulation of actin filament depolymerization
- actin rod assembly
Molecular Function
- magnesium ion binding
- phosphoserine phosphatase activity
- phosphoprotein phosphatase activity
- protein binding
- phosphatase activity
Cellular Component
- cytoplasm
- cytosol
- plasma membrane
- cell-cell junction
- actin cytoskeleton
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000215904
- Coding exons
- 2
- Length
- 8208
- Individuals with no LoFs
- 125429
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 7
- Defined
- 125436
- p
- 0.0000279
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.904 | 78 | 104 | 0.750 | 0.00000680 | 1820 |
| Missense (PolyPhen) | 19 | 31.503 | 0.60311 | 551 | ||
| Synonymous | 0.110 | 48 | 49.0 | 0.980 | 0.00000358 | 688 |
| Loss of Function | 1.23 | 1 | 3.47 | 0.288 | 1.49e-7 | 58 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.000060 | 0.000046 | rare |
| European (Non-Finnish) | 0.000037 | 0.000035 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Protein serine phosphatase that dephosphorylates 'Ser-3' in cofilin and probably also dephosphorylates phospho-serine residues in DSTN. Regulates cofilin-dependent actin cytoskeleton reorganization. Required for normal progress through mitosis and normal cytokinesis. Does not dephosphorylate phospho-threonines in LIMK1. Does not dephosphorylate peptides containing phospho- tyrosine (PubMed:15580268). Pyridoxal phosphate (PLP) phosphatase, which also catalyzes the dephosphorylation of pyridoxine 5'- phosphate (PNP) and pyridoxamine 5'-phosphate (PMP), with order of substrate preference PLP > PNP > PMP (PubMed:14522954). {ECO:0000269|PubMed:14522954, ECO:0000269|PubMed:15580268}.;
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.940
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |