ACP2

acid phosphatase 2, lysosomal, the group of Acid phosphatases

Basic information

Region (hg38): 11:47239301-47248906

Links

ENSG00000134575 ∙ NCBI:53 ∙ OMIM:171650 ∙ HGNC:123 ∙ Uniprot:P11117 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• lysosomal acid phosphatase deficiency (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ACP2 gene.

• Inborn genetic diseases (17 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACP2 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			15	3	1	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	15	3	3

Variants in ACP2

This is a list of pathogenic ClinVar variants found in the ACP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-47240140-G-A			Benign (Mar 30, 2018)
11-47240159-G-A		not specified	Uncertain significance (May 04, 2022)
11-47240167-C-G		not specified	Uncertain significance (Nov 21, 2023)
11-47240169-G-T		not specified	Uncertain significance (Oct 06, 2022)
11-47240211-A-G			Benign (Jul 06, 2018)
11-47242719-T-C			Benign (Jun 16, 2017)
11-47242725-G-A		not specified	Uncertain significance (Apr 12, 2022)
11-47242746-A-C		not specified	Uncertain significance (Jul 13, 2021)
11-47242794-C-T		not specified	Likely benign (Mar 29, 2022)
11-47242854-G-A		not specified	Uncertain significance (Dec 18, 2023)
11-47242867-C-T		not specified	Uncertain significance (Jun 24, 2022)
11-47243128-C-T			Benign (Mar 30, 2018)
11-47243279-G-A		not specified	Uncertain significance (Oct 30, 2023)
11-47243341-G-A			Likely benign (May 10, 2017)
11-47244762-G-T		not specified	Uncertain significance (Aug 08, 2022)
11-47244764-T-C		not specified	Uncertain significance (Feb 03, 2022)
11-47244785-C-T		not specified	Uncertain significance (Jun 24, 2022)
11-47244851-C-T		not specified	Likely benign (Jun 06, 2023)
11-47244859-G-T		not specified	Uncertain significance (Jul 19, 2023)
11-47245491-C-T		not specified	Uncertain significance (Nov 22, 2023)
11-47245501-C-G		not specified	Uncertain significance (Aug 30, 2021)
11-47245506-G-A		not specified	Uncertain significance (May 08, 2023)
11-47245528-C-T			Benign (Mar 16, 2017)
11-47245548-A-G		not specified	Uncertain significance (Jan 03, 2024)
11-47245559-G-A		not specified	Uncertain significance (Aug 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACP2	protein_coding	protein_coding	ENST00000256997	11	9605

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000624	0.995	125649	0	98	125747	0.000390

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.826	234	272	0.859	0.0000173	2722
Missense in Polyphen		83	101.52	0.81756		1115
Synonymous	0.644	100	109	0.921	0.00000668	856
Loss of Function	2.48	11	24.2	0.455	0.00000112	254

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00229	0.00223
Ashkenazi Jewish	0.00	0.00
East Asian	0.000929	0.000925
Finnish	0.00	0.00
European (Non-Finnish)	0.000125	0.000114
Middle Eastern	0.000929	0.000925
South Asian	0.000270	0.000261
Other	0.00150	0.000815

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Note=Lysosomal acid phosphatase has been shown to be deficient in cultured fibroblasts from patients manifesting intermittent vomiting, hypotonia, lethargy, opisthotonos, terminal bleeding and death in early infancy. {ECO:0000269|PubMed:5410815}.
• Pathway: Lysosome - Homo sapiens (human);Riboflavin metabolism - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.465

Intolerance Scores

• loftool: 0.734
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.47

Haploinsufficiency Scores

• pHI: 0.179
• hipred: N
• hipred_score: 0.455
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.994

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Acp2
• 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); growth/size/body region phenotype; cellular phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; skeleton phenotype; renal/urinary system 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: skeletal system development;lysosome organization;dephosphorylation
• Cellular component: lysosome;lysosomal membrane;membrane;integral component of membrane;lysosomal lumen;extracellular exosome
• Molecular function: acid phosphatase activity