PLPP4 phospholipid phosphatase 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PLPP4provided by HGNC
Official Full Name: phospholipid phosphatase 4provided by HGNC
Primary source: HGNC:HGNC:23531
See related: Ensembl:ENSG00000203805 AllianceGenome:HGNC:23531
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
Also known as: DPPL2; PPAPDC1; PPAPDC1A
Summary: Enables diacylglycerol diphosphate phosphatase activity; identical protein binding activity; and phosphatidate phosphatase activity. Involved in phospholipid dephosphorylation and regulation of calcium ion import. Predicted to be located in plasma membrane. Predicted to be active in membrane. Biomarker of breast cancer. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Low expression observed in reference dataset See more
Orthologs: mouse all
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Genomic context

Location:: 10q26.12

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (120456954..120592065)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (121355031..121487934)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (122216466..122351577)

Chromosome 10 - NC_000010.11 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 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?

PPAPDC1A fusions and in-frame fusions containing a RhoGAP domain clearly define the aggressive subset (7.5%) of diffuse gastric cancer.
Title: RhoGAP domain-containing fusions and PPAPDC1A fusions are recurrent and prognostic in diffuse gastric cancer.
Studied the clinical significance and biological roles of PLPP4 in lung carcinoma.
Title: Phospholipid Phosphatase 4 promotes proliferation and tumorigenesis, and activates Ca(2+)-permeable Cationic Channel in lung carcinoma cells.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
DPPL1 and DPPL2 represent a novel type of mammalian phosphatidate phosphatase.
Title: Cloning and characterization of DPPL1 and DPPL2, representatives of a novel type of mammalian phosphatidate phosphatase.

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

EBI GWAS Catalog

Description
Genome-wide association study of the rate of cognitive decline in Alzheimer's disease. 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

RH44621 (e-PCR)
- UniSTS:77881

NoName (e-PCR)
- UniSTS:487229

D10S1757 (e-PCR)
- UniSTS:20820

G60313 (e-PCR)
- UniSTS:137569

U64671 (e-PCR)
- UniSTS:65142

D10S209 (e-PCR)
- UniSTS:60793

SHGC-142790 (e-PCR)
- UniSTS:171661

SHGC-35172 (e-PCR)
- UniSTS:7071

G62583 (e-PCR)
- UniSTS:139710

SHGC-143619 (e-PCR)
- UniSTS:171982

SHGC-147463 (e-PCR)
- UniSTS:175823

D10S209 (e-PCR)
- UniSTS:22503

U64670 (e-PCR)
- UniSTS:4596

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables diacylglycerol diphosphate phosphatase activity	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables phosphatidate phosphatase activity	EXP Inferred from Experiment more info	PubMed
enables phosphatidate phosphatase activity	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidate phosphatase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in Fc-gamma receptor signaling pathway involved in phagocytosis	TAS Traceable Author Statement more info
involved_in blastocyst hatching	IEA Inferred from Electronic Annotation more info
involved_in phospholipid dephosphorylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in phospholipid dephosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in phospholipid metabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in phospholipid metabolic process	IEA Inferred from Electronic Annotation more info
involved_in regulation of calcium ion import	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: phospholipid phosphatase 4

Names: diacylglycerol pyrophosphate like 2; diacylglycerol pyrophosphate phosphatase-like 2; phosphatidate phosphatase PPAPDC1A; phosphatidic acid phosphatase type 2 domain containing 1A; phosphatidic acid phosphatase type 2 domain-containing protein 1A

NP_001025230.1

EC 3.1.3.4

EC 3.6.1.75

NP_001305095.1

EC 3.1.3.4

EC 3.6.1.75

NP_001305096.1

EC 3.1.3.4

EC 3.6.1.75

NP_001305097.1

EC 3.1.3.4

EC 3.6.1.75

NP_001305098.1

EC 3.1.3.4

EC 3.6.1.75

XP_005269649.1

EC 3.1.3.4

EC 3.6.1.75

XP_006717749.1

EC 3.1.3.4

EC 3.6.1.75

XP_011537746.1

EC 3.1.3.4

EC 3.6.1.75

XP_016871310.1

EC 3.1.3.4

EC 3.6.1.75

XP_016871311.1

EC 3.1.3.4

EC 3.6.1.75

XP_016871312.1

EC 3.1.3.4

EC 3.6.1.75

XP_024303630.1

EC 3.1.3.4

EC 3.6.1.75

XP_047280665.1

EC 3.1.3.4

EC 3.6.1.75

XP_047280666.1

EC 3.1.3.4

EC 3.6.1.75

XP_054220958.1

EC 3.1.3.4

EC 3.6.1.75

XP_054220959.1

EC 3.1.3.4

EC 3.6.1.75

XP_054220960.1

EC 3.1.3.4

EC 3.6.1.75

XP_054220961.1

EC 3.1.3.4

EC 3.6.1.75

XP_054220962.1

EC 3.1.3.4

EC 3.6.1.75

XP_054220963.1

EC 3.1.3.4

EC 3.6.1.75

XP_054220964.1

EC 3.1.3.4

EC 3.6.1.75

XP_054220965.1

EC 3.1.3.4

EC 3.6.1.75

XP_054220966.1

EC 3.1.3.4

EC 3.6.1.75

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_001030059.3 → NP_001025230.1 phospholipid phosphatase 4 isoform a

See identical proteins and their annotated locations for NP_001025230.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).

Source sequence(s)

AC023282, BC132787, DR000933, HY340365

Consensus CDS

CCDS41573.1

UniProtKB/Swiss-Prot

A2RU82, Q08EQ2, Q0IIP2, Q495B4, Q5VZY1, Q5VZY2

Related

ENSP00000381302.1, ENST00000398250.6

Conserved Domains (1) summary

cd03390
Location:37 → 225

PAP2_containing_1_like; PAP2, subfamily similar to human phosphatidic_acid_phosphatase_type_2_domain_containing_1. Most likely membrane-associated phosphatidic acid phosphatases. Plant members of this group are constitutively expressed in many tissues and exhibit both ...
NM_001318166.2 → NP_001305095.1 phospholipid phosphatase 4 isoform b

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate exon, resulting in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (b) has a distinct C-terminus and is shorter than isoform a.

Source sequence(s)

AC023282, BC101267, DB473853, DR000933, HY340365

UniProtKB/Swiss-Prot

Q5VZY2

Conserved Domains (1) summary

cl00474
Location:37 → 106

PAP2_like; PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid ...
NM_001318167.2 → NP_001305096.1 phospholipid phosphatase 4 isoform c

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks two alternate exons, resulting in the loss of an in-frame segment in the central coding region, compared to variant 1. The encoded isoform (c) is shorter than isoform a.

Source sequence(s)

AC023282, BC101268, DR000933, HY340365

UniProtKB/Swiss-Prot

Q5VZY2

Conserved Domains (1) summary

cl00474
Location:37 → 162

PAP2_like; PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid ...
NM_001318168.2 → NP_001305097.1 phospholipid phosphatase 4 isoform d

Status: VALIDATED

Description

Transcript Variant: This variant (4) lacks three alternate exons, resulting in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (d) has a distinct C-terminus and is shorter than isoform a.

Source sequence(s)

AC023282, BC101267, DR000933, HY340365

UniProtKB/Swiss-Prot

Q5VZY2
NM_001318169.2 → NP_001305098.1 phospholipid phosphatase 4 isoform e

Status: VALIDATED

Description

Transcript Variant: This variant (5) lacks four alternate exons, resulting in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (e) has a distinct C-terminus and is shorter than isoform a.

Source sequence(s)

AC023282, BC122535, DR000933, HY340365

UniProtKB/Swiss-Prot

Q5VZY2

RNA

NR_134516.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (6) splices out a 5' region and lacks three internal exons, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.

Source sequence(s)

AC073587, BC101269, BI459587, DB495310, HY340365

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000010.11 Reference GRCh38.p14 Primary Assembly

Range

120456954..120592065

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011539444.4 → XP_011537746.1 phospholipid phosphatase 4 isoform X1

Conserved Domains (1) summary

cd03390
Location:35 → 223

PAP2_containing_1_like; PAP2, subfamily similar to human phosphatidic_acid_phosphatase_type_2_domain_containing_1. Most likely membrane-associated phosphatidic acid phosphatases. Plant members of this group are constitutively expressed in many tissues and exhibit both ...
XM_005269592.3 → XP_005269649.1 phospholipid phosphatase 4 isoform X4

Conserved Domains (1) summary

cd03390
Location:37 → 168

PAP2_containing_1_like; PAP2, subfamily similar to human phosphatidic_acid_phosphatase_type_2_domain_containing_1. Most likely membrane-associated phosphatidic acid phosphatases. Plant members of this group are constitutively expressed in many tissues and exhibit both ...
XM_006717686.5 → XP_006717749.1 phospholipid phosphatase 4 isoform X3

Conserved Domains (1) summary

cd03390
Location:37 → 207

PAP2_containing_1_like; PAP2, subfamily similar to human phosphatidic_acid_phosphatase_type_2_domain_containing_1. Most likely membrane-associated phosphatidic acid phosphatases. Plant members of this group are constitutively expressed in many tissues and exhibit both ...
XM_017015823.2 → XP_016871312.1 phospholipid phosphatase 4 isoform X6
XM_047424709.1 → XP_047280665.1 phospholipid phosphatase 4 isoform X2
XM_017015822.2 → XP_016871311.1 phospholipid phosphatase 4 isoform X5

Conserved Domains (1) summary

cd03390
Location:7 → 104

PAP2_containing_1_like; PAP2, subfamily similar to human phosphatidic_acid_phosphatase_type_2_domain_containing_1. Most likely membrane-associated phosphatidic acid phosphatases. Plant members of this group are constitutively expressed in many tissues and exhibit both ...
XM_017015821.3 → XP_016871310.1 phospholipid phosphatase 4 isoform X5

Conserved Domains (1) summary

cd03390
Location:7 → 104

PAP2_containing_1_like; PAP2, subfamily similar to human phosphatidic_acid_phosphatase_type_2_domain_containing_1. Most likely membrane-associated phosphatidic acid phosphatases. Plant members of this group are constitutively expressed in many tissues and exhibit both ...
XM_047424710.1 → XP_047280666.1 phospholipid phosphatase 4 isoform X5
XM_024447862.2 → XP_024303630.1 phospholipid phosphatase 4 isoform X5

Conserved Domains (1) summary

cd03390
Location:7 → 104

PAP2_containing_1_like; PAP2, subfamily similar to human phosphatidic_acid_phosphatase_type_2_domain_containing_1. Most likely membrane-associated phosphatidic acid phosphatases. Plant members of this group are constitutively expressed in many tissues and exhibit both ...