ACP3
protein-codingacid phosphatase 3, the group of Acid phosphatases
Gene summary
This gene encodes an enzyme that catalyzes the conversion of orthophosphoric monoester to alcohol and orthophosphate. It is synthesized under androgen regulation and is secreted by the epithelial cells of the prostate gland. An alternatively spliced transcript variant encoding a longer isoform has been found for this gene. This isoform contains a transmembrane domain and is localized in the plasma membrane-endosomal-lysosomal pathway. [provided by RefSeq, Sep 2008]
- ACPP
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~50.9 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 ACP3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001099.5. 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 | 1 | 3 | |||
| missense | 52 | 4 | 1 | 57 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 53 | 6 | 2 | 61 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001090.2 | 10 | MANE Select | |
| Ensembl | ENSP00000337471.5 | 10 | MANE Select | |
| RefSeq | NP_001127666.1 | 11 | Standard | |
| RefSeq | NP_001278966.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Vitamin B2 (riboflavin) metabolism
- Neutrophil degranulation
- Innate Immune System
- Immune System
Biological Process
- purine nucleobase metabolic process
- thiamine metabolic process
- nucleotide metabolic process
- dephosphorylation
- neutrophil degranulation
Molecular Function
- acid phosphatase activity
- protein binding
- 5'-nucleotidase activity
- phosphatase activity
- thiamine phosphate phosphatase activity
Cellular Component
- extracellular space
- nucleus
- lysosomal membrane
- plasma membrane
- vesicle membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000351273
- Coding exons
- 11
- Length
- 50932
- Individuals with no LoFs
- 125374
- Homozygous LoFs
- 3
- Heterozygous LoFs
- 370
- Defined
- 125747
- p
- 0.00148
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.168 | 221 | 228 | 0.969 | 0.0000115 | 2738 |
| Missense (PolyPhen) | 87 | 84.962 | 1.024 | 997 | ||
| Synonymous | -0.306 | 87 | 83.4 | 1.04 | 0.00000426 | 785 |
| Loss of Function | 0.0111 | 24 | 24.1 | 0.998 | 0.00000122 | 282 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00062 | 0.00062 | rare |
| Latino/Admixed American | 0.0011 | 0.0011 | notable |
| Ashkenazi Jewish | 0.017 | 0.017 | notable |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00091 | 0.00091 | rare |
| South Asian | 0.0012 | 0.0012 | notable |
| Other | 0.0018 | 0.0018 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: A non-specific tyrosine phosphatase that dephosphorylates a diverse number of substrates under acidic conditions (pH 4-6) including alkyl, aryl, and acyl orthophosphate monoesters and phosphorylated proteins. Has lipid phosphatase activity and inactivates lysophosphatidic acid in seminal plasma.;
Recessive Scores
- pRec
- 0.156
Intolerance Scores
- LoFtool
- 0.795
- RVIS EVS
- -0.6
- RVIS percentile EVS
- 17.91
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.905
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |