ACP1

acid phosphatase 1, the group of Acid phosphatases|Class II Cys-based phosphatases

Basic information

Region (hg38): 2:264139-278283

Links

ENSG00000143727 ∙ NCBI:52 ∙ OMIM:171500 ∙ HGNC:122 ∙ Uniprot:P24666 ∙ 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 ACP1 gene.

• not provided (7 variants)
• Inborn genetic diseases (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACP1 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			3		1	4
nonsense			2			2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding					1	1
Total	0	0	5	1	3

Variants in ACP1

This is a list of pathogenic ClinVar variants found in the ACP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-264985-G-T			Benign (May 31, 2018)
2-264987-C-T		not specified	Uncertain significance (Feb 15, 2023)
2-265015-G-A			Benign (Dec 31, 2019)
2-265017-C-T			Benign (Aug 16, 2018)
2-271918-C-T			Likely benign (Jul 04, 2018)
2-271938-A-T		not specified	Uncertain significance (Feb 28, 2023)
2-272207-G-A		not specified	Uncertain significance (Aug 12, 2021)
2-272223-G-A			Uncertain significance (Apr 08, 2016)
2-272250-G-T		not specified	Uncertain significance (May 30, 2023)
2-275180-G-T		not specified	Uncertain significance (Dec 17, 2021)
2-277003-A-G		ACID PHOSPHATASE 1, SOLUBLE, A/B POLYMORPHISM OF	Benign (Aug 12, 2020)
2-277229-G-A			Benign (Jul 04, 2018)
2-277250-G-A			Benign (Aug 15, 2018)
2-277255-A-G		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACP1	protein_coding	protein_coding	ENST00000272067	6	14144

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.75e-8	0.0698	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.249	92	85.5	1.08	0.00000434	1046
Missense in Polyphen		28	28.956	0.967		379
Synonymous	-0.924	37	30.5	1.21	0.00000170	272
Loss of Function	-0.478	11	9.42	1.17	4.65e-7	109

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000482	0.000482
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000618	0.0000615
Middle Eastern	0.000164	0.000163
South Asian	0.000264	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts on tyrosine phosphorylated proteins, low-MW aryl phosphates and natural and synthetic acyl phosphates. Isoform 3 does not possess phosphatase activity.
• Pathway: Adherens junction - Homo sapiens (human);Riboflavin metabolism - Homo sapiens (human);Thiamine metabolism - Homo sapiens (human);Riboflavin Metabolism;VEGFA-VEGFR2 Signaling Pathway;TCR;EGFR1;EPHA2 forward signaling (Consensus)

Recessive Scores

• pRec: 0.547

Intolerance Scores

• loftool: 0.967
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.26

Haploinsufficiency Scores

• pHI: 0.223
• hipred: Y
• hipred_score: 0.769
• ghis: 0.547

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.997

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Acp1
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); immune system phenotype

Zebrafish Information Network

• Gene name: acp1
• Affected structure: pronephric distal late tubule
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: peptidyl-tyrosine dephosphorylation
• Cellular component: cytoplasm;cytoplasmic side of plasma membrane;extracellular exosome
• Molecular function: acid phosphatase activity;protein tyrosine phosphatase activity;non-membrane spanning protein tyrosine phosphatase activity;protein binding