PHOSPHO1 phosphoethanolamine/phosphocholine phosphatase 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PHOSPHO1provided by HGNC
Official Full Name: phosphoethanolamine/phosphocholine phosphatase 1provided by HGNC
Primary source: HGNC:HGNC:16815
See related: Ensembl:ENSG00000173868
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Expression: Biased expression in testis (RPKM 17.3), bone marrow (RPKM 8.3) and 3 other tissues See more
Orthologs: mouse all

Genomic context

Location:: 17q21.32

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
109.20201120	current	GRCh38.p13 (GCF_000001405.39)	17	NC_000017.11 (49223366..49230787, complement)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (47300728..47309009, complement)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

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?

CpG sites located in PHOSPHO1 gene showed differential methylation in association with lipid traits. Genetic variants in PHOSPHO1 gene were also associated with lipid profile.
Title: Identification and validation of seven new loci showing differential DNA methylation related to serum lipid profile: an epigenome-wide approach. The REGICOR study.
DNA methylation at the PHOSPHO1 locus cg02650017 in blood DNA was associated with a decreased risk for future type 2 diabetes.
Title: DNA methylation of loci within ABCG1 and PHOSPHO1 in blood DNA is associated with future type 2 diabetes risk.
REVIEW: role of bone-type tissue-nonspecific alkaline phosphatase and PHOSPO1 in vascular calcification
Title: Role of bone-type tissue-nonspecific alkaline phosphatase and PHOSPO1 in vascular calcification.
Observational study of gene-disease association. (HuGE Navigator)
Title: High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men.
The identification of a novel, alternatively spliced PHOSPHO1 transcript (PHOSPHO1-3a), was described.
Title: Identification of a novel splice variant of the haloacid dehalogenase: PHOSPHO1.
Models of PHOSPHO2 and PHOSPHO1 suggest subtle differences in the charge distributions around the putative substrate entry site and in the location of potential H-bond donors.
Title: Probing the substrate specificities of human PHOSPHO1 and PHOSPHO2.

Submit: New GeneRIF Correction

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
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array. GeneReviews: Not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Homologs of the PHOSPHO1 gene: The PHOSPHO1 gene is conserved in chimpanzee, dog, cow, mouse, rat, chicken, zebrafish, A.thaliana, rice, and frog.
Orthologs from Annotation Pipeline: 322 organisms have orthologs with human gene PHOSPHO1
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
metal ion binding	IEA Inferred from Electronic Annotation more info
phosphatase activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
phosphocholine phosphatase activity	IEA Inferred from Electronic Annotation more info
phosphoethanolamine phosphatase activity	IEA Inferred from Electronic Annotation more info
protein binding	IPI Inferred from Physical Interaction more info	PubMed
pyrophosphatase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
bone mineralization involved in bone maturation	IBA Inferred from Biological aspect of Ancestor more info	PubMed
dephosphorylation	IEA Inferred from Electronic Annotation more info
endochondral ossification	IEA Inferred from Electronic Annotation more info
phosphatidylcholine biosynthetic process	TAS Traceable Author Statement more info
phosphatidylethanolamine biosynthetic process	TAS Traceable Author Statement more info
regulation of bone mineralization	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
cytosol	TAS Traceable Author Statement more info
extracellular matrix	IEA Inferred from Electronic Annotation more info
extracellular membrane-bounded organelle	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: phosphoethanolamine/phosphocholine phosphatase

Names: phosphatase, orphan 1

NP_001137276.1

EC 3.1.3.75

NP_848595.1

EC 3.1.3.75

XP_016879760.1

EC 3.1.3.75

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.

mRNA and Protein(s)

NM_001143804.2 → NP_001137276.1 phosphoethanolamine/phosphocholine phosphatase isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and it encodes the longer protein (isoform 1).

Source sequence(s)

AC004797, AJ457189, BC029931

Consensus CDS

CCDS45726.1

UniProtKB/Swiss-Prot

Q8TCT1

Related

ENSP00000406909.1, ENST00000413580.5

Conserved Domains (2) summary

pfam00702
Location:53 → 241

Hydrolase; haloacid dehalogenase-like hydrolase

pfam06888
Location:52 → 289

Put_Phosphatase; Putative Phosphatase
NM_178500.4 → NP_848595.1 phosphoethanolamine/phosphocholine phosphatase isoform 2

See identical proteins and their annotated locations for NP_848595.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses a different splice site, compared to variant 1, that results in the use of an upstream start codon. The resulting protein (isoform 2) has a shorter and distinct N-terminus when it is compared to isoform 1.

Source sequence(s)

AC004797, AJ457189

Consensus CDS

CCDS11547.1

UniProtKB/Swiss-Prot

Q8TCT1

Related

ENSP00000311925.4, ENST00000310544.8

Conserved Domains (1) summary

pfam06888
Location:27 → 264

Put_Phosphatase; Putative Phosphatase

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20201120

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

Reference GRCh38.p13 Primary Assembly

Genomic

NC_000017.11 Reference GRCh38.p13 Primary Assembly

Range

49223366..49230787 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017024271.1 → XP_016879760.1 phosphoethanolamine/phosphocholine phosphatase isoform X1

Conserved Domains (2) summary

pfam00702
Location:111 → 299

Hydrolase; haloacid dehalogenase-like hydrolase

pfam06888
Location:110 → 347

Put_Phosphatase; Putative Phosphatase