ARPP21

protein-coding

cAMP 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

NM_001385562.1

Inheritance

AD

ClinVar variants

P:1U:102B:5

Top phenotype

Monomelic amyotrophy

gnomAD constraint

pLI —, LoF o/e 0.28

Max pathogenic AF

—

Genomic locus

chr3:35,638,945-35,794,496

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~155.6 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

amyotrophic lateral sclerosisLIMITED

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

4 Conditions Cataloged
not specifiedTotal: 97
not providedTotal: 5
Monomelic amyotrophyTotal: 1
Prostate cancerTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
3
clinvar
6
missense
1
clinvar
99
clinvar
2
clinvar
102
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total0110250108

Highest pathogenic variant AF is 0.000002889902

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 152 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001385562.1RefSeqNP_001372491.119MANE Select
ENST00000684406.1EnsemblENSP00000506922.119MANE Select
NM_001025068.1RefSeqNP_001020239.14Standard
NM_001025069.1RefSeqNP_001020240.14Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.2614324480.9650.00002315302
Missense (PolyPhen)88116.540.755131407
Synonymous0.8321581720.9190.000009901571
Loss of Function4.601347.10.2760.00000232507

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000800.00080rare
Latino/Admixed American0.0000870.000087rare
Ashkenazi Jewish0.000100.000099rare
East Asian0.000270.00027rare
Finnish0.000140.00014rare
European (Non-Finnish)0.0000890.000088rare
South Asian0.000100.000098rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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