ACP1

protein-coding

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

Gene summary

The product of this gene belongs to the phosphotyrosine protein phosphatase family of proteins. It functions as an acid phosphatase and a protein tyrosine phosphatase by hydrolyzing protein tyrosine phosphate to protein tyrosine and orthophosphate. This enzyme also hydrolyzes orthophosphoric monoesters to alcohol and orthophosphate. This gene is genetically polymorphic, and three common alleles segregating at the corresponding locus give rise to six phenotypes. Each allele appears to encode at least two electrophoretically different isozymes, Bf and Bs, which are produced in allele-specific ratios. Multiple alternatively spliced transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Aug 2008]

MANE transcript

NM_004300.4

Inheritance

—

ClinVar variants

U:15B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.17

Max pathogenic AF

—

Genomic locus

chr2:264,140-278,283

External References & Databases

Ensembl (ENSG00000143727)

Transcript & Mutation Effects

hg38 • Region Span ~14.1 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ACP1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 12

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004300.4. 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.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	2 clinvar	3
missense			9 clinvar		1 clinvar	10
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	15	1	3	19

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 54 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004300.4	RefSeq	NP_004291.1	6	MANE Select
ENST00000272065.10	Ensembl	ENSP00000272065.5	6	MANE Select
NM_001040649.3	RefSeq	NP_001035739.1	3	Standard
NM_007099.4	RefSeq	NP_009030.1	6	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
acp1	Danio rerio	Structure: pronephric distal late tubule Quality: decreased length abnormal

Gene / Model

Organism

Observed Phenotype

acp1

Danio rerio

Structure: pronephric distal late tubule

Quality: decreased length

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Adherens junction - Homo sapiens (human)
Riboflavin metabolism - Homo sapiens (human)
Thiamine metabolism - Homo sapiens (human)
Riboflavin Metabolism
VEGFA-VEGFR2 Signaling Pathway

Biological Process

peptidyl-tyrosine dephosphorylation

Molecular Function

acid phosphatase activity
protein tyrosine phosphatase activity
non-membrane spanning protein tyrosine phosphatase activity
protein binding

Cellular Component

cytoplasm
cytoplasmic side of plasma membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000272067
Coding exons: 6
Length: 14144
Individuals with no LoFs: 125719
Homozygous LoFs: 0
Heterozygous LoFs: 29
Defined: 125748
p: 0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.249	92	85.5	1.08	0.00000434	1046
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.00026	0.00026	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.547

Intolerance Scores

LoFtool: 0.967
RVIS EVS: 0.26
RVIS percentile EVS: 70.26

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.997

Gene Damage Prediction

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