ARPP21
protein-codingcAMP regulated phosphoprotein 21, the group of MicroRNA protein coding host genes
Gene summary
This gene encodes a cAMP-regulated phosphoprotein. The encoded protein is enriched in the caudate nucleus and cerebellar cortex. A similar protein in mouse may be involved in regulating the effects of dopamine in the basal ganglia. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jun 2012]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~155.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0004976
Submitter: ClinGen
*ARPP21* was first reported in relation to autosomal dominant amyotrophic lateral sclerosis (ALS) in 2019 (Cooper-Knock et al., PMID: 30811981). In humans, ARPP21 was initially identified as a 9.6 kDa protein that regulates calcium/calmodulin-dependent signaling (Rakhilin et al., PMID 15499021). A long isoform of ARPP21 appears to function in post-transcriptional regulation of gene expression (Rehfeld et al., PMID 29581509, Halbout et al., PMID 37507022). Nine missense variants that have been reported in 17 probands in four publications (PMIDs: 30811981, 31653410, 35525134, 38960585) are included in this curation. The mechanism of pathogenicity is unknown. This gene-disease association is also supported by expression studies and *in vitro* functional assays (PMIDs: 8120638, 29581509). ARPP21 is predominantly expressed in a subset of brain tissues (PMID 8120638). Endogenous ARPP21 in cultured mouse cortical neurons localizes to stress granules after arsenite treatment (PMID 29581509). This gene-disease pair was originally evaluated by the Amyotrophic Lateral Sclerosis Spectrum Disorders GCEP on January 10, 2023. It was reevaluated on January 14, 2025. As a result of this reevaluation, the classification did not change. New evidence was added to the curation, but it was not strong enough to change the classification. In summary, there is limited evidence to support this gene-disease relationship. Although more evidence is needed to support a causal role, no convincing evidence has emerged that contradicts the gene-disease relationship. This classification was approved by the ClinGen ALS GCEP on the meeting date January 14, 2025 (SOP Version 11).
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ARPP21 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001385562.1. 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 | 3 | 3 | 6 | |||
| missense | 1 | 99 | 2 | 102 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 1 | 102 | 5 | 0 | 108 |
Highest pathogenic variant AF is 0.000002889902
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001372491.1 | 19 | MANE Select | |
| Ensembl | ENSP00000506922.1 | 19 | MANE Select | |
| RefSeq | NP_001020239.1 | 4 | Standard | |
| RefSeq | NP_001020240.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- biological_process
- cellular response to heat
Molecular Function
- molecular_function
- nucleic acid binding
- calmodulin binding
Cellular Component
- cellular_component
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000458225
- Coding exons
- 18
- Length
- 155552
- Individuals with no LoFs
- 125710
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 38
- Defined
- 125748
- p
- 0.000151
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.261 | 432 | 448 | 0.965 | 0.0000231 | 5302 |
| Missense (PolyPhen) | 88 | 116.54 | 0.75513 | 1407 | ||
| Synonymous | 0.832 | 158 | 172 | 0.919 | 0.00000990 | 1571 |
| Loss of Function | 4.60 | 13 | 47.1 | 0.276 | 0.00000232 | 507 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00080 | 0.00080 | rare |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.00027 | 0.00027 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.000089 | 0.000088 | rare |
| South Asian | 0.00010 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Isoform 2 may act as a competitive inhibitor of calmodulin-dependent enzymes such as calcineurin in neurons. {ECO:0000250}.;
Intolerance Scores
- LoFtool
- 0.354
- RVIS EVS
- -0.18
- RVIS percentile EVS
- 40.56
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |