PLD4 phospholipase D family member 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PLD4provided by HGNC
Official Full Name: phospholipase D family member 4provided by HGNC
Primary source: HGNC:HGNC:23792
See related: Ensembl:ENSG00000166428 MIM:618488; AllianceGenome:HGNC:23792
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: C14orf175
Summary: Predicted to enable single-stranded DNA 5'-3' DNA exonuclease activity. Predicted to be involved in hematopoietic progenitor cell differentiation; phagocytosis; and regulation of cytokine production involved in inflammatory response. Predicted to act upstream of or within establishment of localization in cell. Predicted to be located in early endosome and endoplasmic reticulum membrane. Predicted to be active in several cellular components, including endoplasmic reticulum; phagocytic vesicle; and trans-Golgi network membrane. [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in skin (RPKM 31.7), spleen (RPKM 4.6) and 9 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 14q32.33

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	14	NC_000014.9 (104924879..104937785)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	14	NC_060938.1 (99170773..99184262)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (105391216..105404122)

Chromosome 14 - NC_000014.9 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?

Phospholipase D4 as a signature of toll-like receptor 7 or 9 signaling is expressed on blastic T-bet + B cells in systemic lupus erythematosus.
Title: Phospholipase D4 as a signature of toll-like receptor 7 or 9 signaling is expressed on blastic T-bet + B cells in systemic lupus erythematosus.
PLD4 is a genetic determinant to systemic lupus erythematosus.
Title: PLD4 is a genetic determinant to systemic lupus erythematosus and involved in murine autoimmune phenotypes.
PLD4 expression in colon cancer tissues
Title: PLD4 promotes M1 macrophages to perform antitumor effects in colon cancer cells.
We determined that PLD4 is a novel susceptibility gene for sysetmic sclerosis in Japanese, thus confirming the involvement of PLD4 in autoimmunity.
Title: PLD4 as a novel susceptibility gene for systemic sclerosis in a Japanese population.

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
Genetics of rheumatoid arthritis contributes to biology and drug discovery. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis identifies nine new loci associated with rheumatoid arthritis in the Japanese population. 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

MARC_16895-16896:1020711008:1 (e-PCR)
- UniSTS:268147

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
NOT enables phospholipase D activity	ISS Inferred from Sequence or Structural Similarity more info
enables single-stranded DNA 5'-3' DNA exonuclease activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in DNA metabolic process	IEA Inferred from Electronic Annotation more info
involved_in establishment of localization in cell	IEA Inferred from Electronic Annotation more info
involved_in hematopoietic progenitor cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in inflammatory response	IEA Inferred from Electronic Annotation more info
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
involved_in phagocytosis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within phagocytosis	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of cytokine production involved in inflammatory response	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in early endosome	ISS Inferred from Sequence or Structural Similarity more info
is_active_in endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
is_active_in phagocytic vesicle	IBA Inferred from Biological aspect of Ancestor more info
located_in phagocytic vesicle	ISS Inferred from Sequence or Structural Similarity more info
is_active_in trans-Golgi network membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in trans-Golgi network membrane	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: 5'-3' exonuclease PLD4

Names: PLD 4; choline phosphatase 4; phosphatidylcholine-hydrolyzing phospholipase D4; phospholipase D4

NP_001295103.1

EC 3.1.16.1

NP_620145.2

EC 3.1.16.1

XP_011534713.1

EC 3.1.16.1

XP_054231322.1

EC 3.1.16.1

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_001308174.2 → NP_001295103.1 5'-3' exonuclease PLD4 isoform 1

Status: VALIDATED

Description

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

Source sequence(s)

AK295352, AK296188, AL512802, AW104909, DC328186

Consensus CDS

CCDS76725.1

UniProtKB/TrEMBL

B4DJQ6, F5H2B5

Related

ENSP00000438677.1, ENST00000540372.5

Conserved Domains (3) summary

cd09145
Location:105 → 274

PLDc_vPLD4_1; Putative catalytic domain, repeat 1, of vertebrate phospholipase PLD4

cd09148
Location:311 → 497

PLDc_vPLD4_2; Putative catalytic domain, repeat 2, of vertebrate phospholipase PLD4

PHA02820
Location:99 → 509

PHA02820; phospholipase-D-like protein; Provisional
NM_138790.5 → NP_620145.2 5'-3' exonuclease PLD4 isoform 2

See identical proteins and their annotated locations for NP_620145.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and uses an alternate splice site in the 5' coding region that results in use of a downstream start codon compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.

Source sequence(s)

AY358843

Consensus CDS

CCDS9995.2

UniProtKB/Swiss-Prot

Q6UWD2, Q96BZ4

UniProtKB/TrEMBL

B4DI07

Related

ENSP00000376372.5, ENST00000392593.9

Conserved Domains (3) summary

cd09148
Location:304 → 490

PLDc_vPLD4_2; Putative catalytic domain, repeat 2, of vertebrate phospholipase PLD4

PHA02820
Location:92 → 502

PHA02820; phospholipase-D-like protein; Provisional

cl15239
Location:98 → 267

PLDc_SF; Catalytic domain of phospholipase D superfamily proteins

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_000014.9 Reference GRCh38.p14 Primary Assembly

Range

104924879..104937785

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011536411.3 → XP_011534713.1 5'-3' exonuclease PLD4 isoform X1

UniProtKB/TrEMBL

A0A3B3IT68

Related

ENSP00000497627.1, ENST00000649344.1

Conserved Domains (4) summary

cd09145
Location:105 → 274

PLDc_vPLD4_1; Putative catalytic domain, repeat 1, of vertebrate phospholipase PLD4

COG1502
Location:218 → 440

Cls; Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase or related enzyme [Lipid transport and metabolism]

pfam13091
Location:130 → 272

PLDc_2; PLD-like domain

cl15239
Location:311 → 447

PLDc_SF; Catalytic domain of phospholipase D superfamily proteins