ARPP21

cAMP regulated phosphoprotein 21, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 3:35638945-35794496

Links

ENSG00000172995 ∙ NCBI:10777 ∙ OMIM:605488 ∙ HGNC:16968 ∙ Uniprot:Q9UBL0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• amyotrophic lateral sclerosis (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ARPP21 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARPP21 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			32	1		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	3	0

Variants in ARPP21

This is a list of pathogenic ClinVar variants found in the ARPP21 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-35681854-G-T		not specified	Uncertain significance (Sep 22, 2023)
3-35687748-C-G		not specified	Uncertain significance (Jan 22, 2024)
3-35687757-C-A		not specified	Uncertain significance (Nov 08, 2022)
3-35687797-G-A			Uncertain significance (Jun 01, 2023)
3-35690130-G-A		not specified	Uncertain significance (Feb 23, 2023)
3-35690935-T-C		not specified	Uncertain significance (Jan 26, 2022)
3-35690984-A-G		not specified	Uncertain significance (Oct 03, 2022)
3-35690990-C-A		not specified	Uncertain significance (Dec 08, 2021)
3-35706991-G-C		not specified	Uncertain significance (Mar 30, 2024)
3-35707034-G-A		not specified	Likely benign (Mar 30, 2024)
3-35708980-G-C		not specified	Uncertain significance (Mar 20, 2023)
3-35715459-C-G		not specified	Uncertain significance (Apr 06, 2022)
3-35717300-G-A		not specified	Uncertain significance (Oct 29, 2021)
3-35717327-A-G		not specified	Uncertain significance (Mar 25, 2024)
3-35717352-C-G			Likely benign (Feb 01, 2023)
3-35721618-G-C		not specified	Uncertain significance (Feb 26, 2024)
3-35721633-T-A		not specified	Uncertain significance (Nov 17, 2022)
3-35721637-G-A		not specified	Uncertain significance (Oct 17, 2023)
3-35729327-G-A		not specified	Uncertain significance (Aug 08, 2023)
3-35729375-C-T		not specified	Uncertain significance (Nov 22, 2021)
3-35729395-G-A		not specified	Uncertain significance (Oct 02, 2023)
3-35729404-C-G		not specified	Uncertain significance (Dec 08, 2022)
3-35729427-G-C		not specified	Uncertain significance (Jul 22, 2022)
3-35729430-T-A		not specified	Uncertain significance (Mar 01, 2024)
3-35729432-G-T		Malignant tumor of prostate	Uncertain significance (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARPP21	protein_coding	protein_coding	ENST00000458225	18	155552

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0120	0.988	125710	0	38	125748	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.261	432	448	0.965	0.0000231	5302
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000889	0.000887
Ashkenazi Jewish	0.0000997	0.0000992
East Asian	0.000275	0.000272
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000887	0.0000879
Middle Eastern	0.000275	0.000272
South Asian	0.000102	0.0000980
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.552
• ghis: 0.480

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Arpp21
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: biological_process;cellular response to heat
• Cellular component: cellular_component;cytoplasm
• Molecular function: molecular_function;nucleic acid binding;calmodulin binding