ACP3

acid phosphatase 3, the group of Acid phosphatases

Basic information

Region (hg38): 3:132317369-132368302

Previous symbols: [ "ACPP" ]

Links

ENSG00000014257 ∙ NCBI:55 ∙ OMIM:171790 ∙ HGNC:125 ∙ Uniprot:P15309 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ACP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACP3 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				1	1	2
missense			20		1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	20	1	2

Variants in ACP3

This is a list of pathogenic ClinVar variants found in the ACP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-132317466-G-A		not specified	Uncertain significance (Aug 10, 2021)
3-132317481-G-A		not specified	Uncertain significance (Dec 09, 2023)
3-132317527-T-C		not specified	Uncertain significance (Sep 01, 2021)
3-132328263-T-C			Likely benign (Mar 29, 2018)
3-132328294-A-G		not specified	Uncertain significance (Nov 30, 2022)
3-132328301-C-T		not specified	Uncertain significance (Sep 26, 2024)
3-132328319-T-C		not specified	Uncertain significance (Oct 11, 2024)
3-132328324-G-C		not specified	Uncertain significance (Jan 24, 2023)
3-132328360-C-G		not specified	Uncertain significance (Jan 02, 2024)
3-132331678-A-G		not specified	Uncertain significance (Oct 02, 2023)
3-132331684-T-C		not specified	Uncertain significance (Jun 11, 2021)
3-132332213-G-A		not specified	Likely benign (Apr 09, 2024)
3-132332219-C-T		not specified	Uncertain significance (Jan 26, 2023)
3-132332220-G-A		not specified	Uncertain significance (Aug 08, 2023)
3-132332238-T-C		not specified	Uncertain significance (Jan 27, 2022)
3-132332270-G-T		not specified	Uncertain significance (Mar 25, 2024)
3-132332272-T-C			Benign (May 25, 2018)
3-132332297-C-A		not specified	Uncertain significance (Aug 04, 2024)
3-132332307-C-T		not specified	Uncertain significance (May 15, 2024)
3-132337468-C-T		not specified	Uncertain significance (Jun 19, 2024)
3-132337474-A-G		not specified	Uncertain significance (Apr 12, 2022)
3-132337486-C-T		not specified	Uncertain significance (May 08, 2024)
3-132337495-G-A		not specified	Uncertain significance (Sep 14, 2023)
3-132337518-A-G			Likely benign (Jun 06, 2018)
3-132342627-G-A		not specified	Uncertain significance (Oct 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACP3	protein_coding	protein_coding	ENST00000351273	11	50932

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.55e-16	0.00868	125374	3	370	125747	0.00148

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.168	221	228	0.969	0.0000115	2738
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00173	0.00173
Ashkenazi Jewish	0.0173	0.0169
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000912	0.000906
Middle Eastern	0.000218	0.000217
South Asian	0.00125	0.00124
Other	0.00181	0.00179

dbNSFP

Source: dbNSFP

• 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.
• Pathway: Vitamin B2 (riboflavin) metabolism;Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.156

Intolerance Scores

• loftool: 0.795
• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.91

Haploinsufficiency Scores

• pHI: 0.185
• hipred: N
• hipred_score: 0.440
• ghis: 0.421

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.905

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Acpp
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; neoplasm; endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: purine nucleobase metabolic process;thiamine metabolic process;nucleotide metabolic process;dephosphorylation;neutrophil degranulation;adenosine metabolic process;protein homotetramerization;regulation of sensory perception of pain;positive regulation of adenosine receptor signaling pathway
• Cellular component: extracellular space;nucleus;lysosomal membrane;plasma membrane;vesicle membrane;integral component of membrane;filopodium;azurophil granule membrane;extracellular exosome
• Molecular function: acid phosphatase activity;protein binding;5'-nucleotidase activity;phosphatase activity;thiamine phosphate phosphatase activity;identical protein binding;protein homodimerization activity;lysophosphatidic acid phosphatase activity