SGPP2 sphingosine-1-phosphate phosphatase 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SGPP2provided by HGNC
Official Full Name: sphingosine-1-phosphate phosphatase 2provided by HGNC
Primary source: HGNC:HGNC:19953
See related: Ensembl:ENSG00000163082 MIM:612827; AllianceGenome:HGNC:19953
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: SPP2; SPPase2
Summary: The protein encoded by this gene is a transmembrane protein that degrades the bioactive signaling molecule sphingosine 1-phosphate. The encoded protein is induced during inflammatory responses and has been shown to be downregulated by the microRNA-31 tumor suppressor. Alternative splice variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2016]
Expression: Broad expression in thyroid (RPKM 13.7), esophagus (RPKM 12.0) and 18 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q36.1

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (222423988..222562621)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (222909191..223047956)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (223288707..223427340)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

SGPP2, a sphingosine-1-phosphate phosphatase, is a novel vitamin D-responsive gene associated with lung function.
Title: Vitamin D-responsive SGPP2 variants associated with lung cell expression and lung function.
characterization of SPP2, another member of the SPP family that may play a role in attenuating intracellular S1P signaling.
Title: Identification and characterization of a novel human sphingosine-1-phosphate phosphohydrolase, hSPP2.
This study provides detailed insights into the regulation of SPP2 gene expression and suggests that SPP2 might be a novel player in pro-inflammatory signalling.
Title: Sphingosine 1-phosphate phosphatase 2 is induced during inflammatory responses.

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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

EBI GWAS Catalog

Description
Genetic variants associated with disordered eating. EBI GWAS Catalog EBI GWAS CatalogPubMed

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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Markers

SHGC-141517 (e-PCR)
- UniSTS:183296

SHGC-83242 (e-PCR)
- UniSTS:101135

NoName (e-PCR)
- UniSTS:490006

SHGC-146400 (e-PCR)
- UniSTS:172600

SHGC-153751 (e-PCR)
- UniSTS:183371

RH122791 (e-PCR)
- UniSTS:135026

G63032 (e-PCR)
- UniSTS:140157

D11S3114 (e-PCR)
- UniSTS:152207

D2S2300 (e-PCR), detects polymorphism
- UniSTS:4545

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables dihydrosphingosine-1-phosphate phosphatase activity	TAS Traceable Author Statement more info
enables sphingosine-1-phosphate phosphatase activity	IBA Inferred from Biological aspect of Ancestor more info
enables sphingosine-1-phosphate phosphatase activity	IDA Inferred from Direct Assay more info	PubMed
enables sphingosine-1-phosphate phosphatase activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in phospholipid dephosphorylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of type B pancreatic cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in sphingolipid catabolic process	TAS Traceable Author Statement more info
involved_in sphingosine metabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in sphingosine metabolic process	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
is_active_in endoplasmic reticulum membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: sphingosine-1-phosphate phosphatase 2

Names: sphingosine 1-phosphate phosphohydrolase 2; sphingosine-1-phosphatase 2; sphingosine-1-phosphate phosphotase 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.

mRNA and Protein(s)

NM_001320833.2 → NP_001307762.1 sphingosine-1-phosphate phosphatase 2 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (2) contains an alternate exon in the 5' end compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2 and 3 both encode the same isoform (b).

Source sequence(s)

AC097461, AK314322, BC114513, BU676534

UniProtKB/TrEMBL

Q4ZFX2

Conserved Domains (2) summary

COG0671
Location:1 → 108

PgpB; Membrane-associated phospholipid phosphatase [Lipid transport and metabolism]

cd03388
Location:1 → 105

PAP2_SPPase1; PAP2_like proteins, sphingosine-1-phosphatase subfamily. Sphingosine-1-phosphatase is an intracellular enzyme located in the endoplasmic reticulum, which regulates the level of sphingosine-1-phosphate (S1P), a bioactive lipid. S1P acts as a second ...
NM_001320834.2 → NP_001307763.1 sphingosine-1-phosphate phosphatase 2 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2 and 3 both encode the same isoform (b)

Source sequence(s)

AC097461, AC112718, AK096323, BU676534

UniProtKB/TrEMBL

Q4ZFX2

Conserved Domains (2) summary

COG0671
Location:1 → 108

PgpB; Membrane-associated phospholipid phosphatase [Lipid transport and metabolism]

cd03388
Location:1 → 105

PAP2_SPPase1; PAP2_like proteins, sphingosine-1-phosphatase subfamily. Sphingosine-1-phosphatase is an intracellular enzyme located in the endoplasmic reticulum, which regulates the level of sphingosine-1-phosphate (S1P), a bioactive lipid. S1P acts as a second ...
NM_152386.4 → NP_689599.2 sphingosine-1-phosphate phosphatase 2 isoform a

See identical proteins and their annotated locations for NP_689599.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (a).

Source sequence(s)

AC097461, AF542512, AK314322, BU676534

Consensus CDS

CCDS2453.1

UniProtKB/Swiss-Prot

A3KPB4, Q8IWX5, Q8N8Q6

UniProtKB/TrEMBL

Q3B870

Related

ENSP00000315137.7, ENST00000321276.8

Conserved Domains (1) summary

cd03388
Location:84 → 233

PAP2_SPPase1; PAP2_like proteins, sphingosine-1-phosphatase subfamily. Sphingosine-1-phosphatase is an intracellular enzyme located in the endoplasmic reticulum, which regulates the level of sphingosine-1-phosphate (S1P), a bioactive lipid. S1P acts as a second ...