ACP2 acid phosphatase 2, lysosomal [Homo sapiens (human)] - Gene

Summary

Official Symbol: ACP2provided by HGNC
Official Full Name: acid phosphatase 2, lysosomalprovided by HGNC
Primary source: HGNC:HGNC:123
See related: Ensembl:ENSG00000134575 MIM:171650; AllianceGenome:HGNC:123
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: LAP
Summary: The protein encoded by this gene belongs to the histidine acid phosphatase family, which hydrolyze orthophosphoric monoesters to alcohol and phosphate. This protein is localized to the lysosomal membrane, and is chemically and genetically distinct from the red cell acid phosphatase. Mice lacking this gene showed multiple defects, including bone structure alterations, lysosomal storage defects, and an increased tendency towards seizures. An enzymatically-inactive allele of this gene in mice showed severe growth retardation, hair-follicle abnormalities, and an ataxia-like phenotype. Alternatively spliced transcript variants have been found for this gene. A C-terminally extended isoform is also predicted to be produced by the use of an alternative in-frame translation termination codon via a stop codon readthrough mechanism. [provided by RefSeq, Oct 2017]
Expression: Ubiquitous expression in duodenum (RPKM 19.4), placenta (RPKM 17.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11p11.2; 11p12-p11

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (47239302..47248814, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (47396045..47405572, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (47260853..47270365, complement)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Clinical and molecular evaluation of 13 Brazilian patients with Gomez-Lopez-Hernandez syndrome.
Title: Clinical and molecular evaluation of 13 Brazilian patients with Gomez-López-Hernández syndrome.
In addition to replicating a previously identified genome-wide significant locus for corneal astigmatism near the PDGFRA gene, gene-based analysis identified three novel candidate genes, CLDN7, ACP2, and TNFAIP8L3, that warrant further investigation to understand their role in the pathogenesis of corneal astigmatism. (Meta-analysis)
Title: A genome-wide association study of corneal astigmatism: The CREAM Consortium.
Data show that lysosomal acid phosphatase 2 (ACP2) was overexpressed in colorectal cancer (CRC) and associated with poor outcome in stage II CRC, and that high expression of ACP2 patients were more sensitive to chemotherapy than those with a low expression, suggesting ACP2 as a marker for CRC patients receiving chemotherapy.
Title: Lysosomal acid phosphatase 2 is an unfavorable prognostic factor but is associated with better survival in stage II colorectal cancer patients receiving chemotherapy.
An enzymatically inactive allele of mouse Acp2 causes cerebellum abnormalities, growth retardation, hair-follicle abnormalities, and an ataxia-like phenotype.
Title: Mutation in the gene encoding lysosomal acid phosphatase (Acp2) causes cerebellum and skin malformation in mouse.
LAP-deficient mice exhibit multiple defects including bone structure alterations, lysosomal storage defects in the kidneys and central nervous system, and an increased tendency towards seizures.
Title: Mice deficient in lysosomal acid phosphatase develop lysosomal storage in the kidney and central nervous system.
Observational study of gene-disease association. (HuGE Navigator)
Title: Polymorphisms in mitochondrial genes and prostate cancer risk.
Genome-wide association study of gene-disease association. (HuGE Navigator)
Title: Identification of a novel risk locus for progressive supranuclear palsy by a pooled genomewide scan of 500,288 single-nucleotide polymorphisms.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Acid phosphatase deficiency MedGen: C0268410 OMIM: 200950 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of acid phosphatase 2, lysosomal (ACP2) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH18246 (e-PCR)
- UniSTS:16145

G54107 (e-PCR)
- UniSTS:109344

GDB:197878 (e-PCR)
- UniSTS:155983

D11S4389 (e-PCR)
- UniSTS:16213

RH27445 (e-PCR)
- UniSTS:89986

RH79156 (e-PCR)
- UniSTS:50847

RH27367 (e-PCR)
- UniSTS:87734

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables acid phosphatase activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in dephosphorylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in lysosome organization	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in extracellular exosome	HDA more info	PubMed
located_in lysosomal lumen	IEA Inferred from Electronic Annotation more info
located_in lysosomal membrane	IEA Inferred from Electronic Annotation more info
is_active_in lysosome	IBA Inferred from Biological aspect of Ancestor more info
located_in lysosome	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	HDA more info	PubMed

General protein information

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Preferred Names: lysosomal acid phosphatase

NP_001289418.1

EC 3.1.3.2

NP_001289419.1

EC 3.1.3.2

NP_001289420.1

EC 3.1.3.2

NP_001289421.1

EC 3.1.3.2

NP_001343945.1

EC 3.1.3.2

NP_001601.1

EC 3.1.3.2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_023296.2 RefSeqGene

Range

5000..14512

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001302489.2 → NP_001289418.1 lysosomal acid phosphatase isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) contains an alternate 5' terminal exon, and initiates translation at an alternate translation start codon compared to variant 1. The encoded shorter isoform (3) has a distinct N-terminus compared to isoform 1.

Source sequence(s)

AC018410

Consensus CDS

CCDS76402.1

UniProtKB/TrEMBL

B7Z552, E9PQY3

Related

ENSP00000432439.1, ENST00000533929.7

Conserved Domains (1) summary

cd07061
Location:11 → 302

HP_HAP_like; Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction
NM_001302490.2 → NP_001289419.1 lysosomal acid phosphatase isoform 4 precursor

See identical proteins and their annotated locations for NP_001289419.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks an in-frame exon in the 5' coding region compared to variant 1. The encoded shorter isoform (4) lacks an internal protein segment compared to isoform 1.

Source sequence(s)

AC018410

Consensus CDS

CCDS76403.1

UniProtKB/TrEMBL

B7Z6L8, B7Z7D2

Related

ENSP00000432205.1, ENST00000527256.7

Conserved Domains (1) summary

cl11399
Location:37 → 298

HP; Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction
NM_001302491.2 → NP_001289420.1 lysosomal acid phosphatase isoform 5 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks two consecutive in-frame exons in the 5' coding region compared to variant 1. The encoded shorter isoform (5) lacks an internal protein segment compared to isoform 1.

Source sequence(s)

AC018410

Consensus CDS

CCDS76404.1

UniProtKB/TrEMBL

B7Z4Z2, E9PHY0

Related

ENSP00000436658.1, ENST00000529444.7

Conserved Domains (1) summary

cd07061
Location:33 → 267

HP_HAP_like; Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction
NM_001302492.2 → NP_001289421.1 lysosomal acid phosphatase isoform 6

Status: REVIEWED

Description

Transcript Variant: This variant (6) lacks an internal exon and uses an alternate acceptor splice site in the 5' region compared to variant 1. These differences result in translation initiation at an in-frame downstream start codon compared to variant 1. The encoded isoform (6) has a shorter N-terminus compared to isoform 1.

Source sequence(s)

AC018410

UniProtKB/TrEMBL

B7Z8T9

Conserved Domains (1) summary

cd07061
Location:16 → 143

HP_HAP_like; Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction
NM_001357016.2 → NP_001343945.1 lysosomal acid phosphatase isoform 1x precursor

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the predominant transcript and encodes two isoforms, which result from the use of alternative in-frame translation termination codons. The shorter isoform (1) results from translation termination at the upstream UGA stop codon, while the longer isoform (1x) results from UGA stop codon readthrough to the downstream UAG termination codon. This RefSeq represents the longer isoform (1x). As the UGA stop codon has been reported to specify several alternative amino acids (tryptophan, cysteine, arginine and serine), its location in the longer isoform is denoted by an 'X'.

Source sequence(s)

AC018410

Consensus CDS

CCDS91470.1

UniProtKB/TrEMBL

A0A5F9ZHR7, B7Z6L8

Related

ENSP00000500571.2, ENST00000672636.2

Conserved Domains (1) summary

cd07061
Location:33 → 330

HP_HAP_like; Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction
NM_001610.4 → NP_001601.1 lysosomal acid phosphatase isoform 1 precursor

See identical proteins and their annotated locations for NP_001601.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the predominant transcript and encodes two isoforms, which result from the use of alternative in-frame translation termination codons. The shorter isoform (1) results from translation termination at the upstream UGA stop codon, while the longer isoform (1x) results from UGA stop codon readthrough to the downstream UAG termination codon. This RefSeq represents the shorter isoform (1).

Source sequence(s)

AC018410

Consensus CDS

CCDS7928.1

UniProtKB/Swiss-Prot

E9PCI1, P11117, Q561W5, Q9BTU7

UniProtKB/TrEMBL

B7Z6L8

Related

ENSP00000500291.1, ENST00000672073.1

Conserved Domains (1) summary

cd07061
Location:33 → 330

HP_HAP_like; Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

47239302..47248814 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

RNA

XR_007062487.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060935.1 Alternate T2T-CHM13v2.0

Range

47396045..47405572 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

RNA

XR_008488405.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001131064.1: Suppressed sequence

Description

NM_001131064.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.