PEDS1 plasmanylethanolamine desaturase 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PEDS1provided by HGNC
Official Full Name: plasmanylethanolamine desaturase 1provided by HGNC
Primary source: HGNC:HGNC:16735
See related: Ensembl:ENSG00000240849 MIM:610994; AllianceGenome:HGNC:16735
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: KUA; CarF; TMEM189
Summary: Co-transcription of this gene and the neighboring downstream gene (ubiquitin-conjugating enzyme E2 variant 1) generates a rare read-through transcript, which encodes a fusion protein comprised of sequence sharing identity with each individual gene product. The protein encoded by this individual gene lacks a UEV1 domain but includes three transmembrane regions. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2009]
Expression: Ubiquitous expression in placenta (RPKM 19.8), esophagus (RPKM 14.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 20q13.13

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (50118254..50153723, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (51888041..51923515, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (48734791..48770260, complement)

Chromosome 20 - NC_000020.11 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?

TMEM189 promotes breast cancer through inhibition of autophagy-regulated ferroptosis.
Title: TMEM189 promotes breast cancer through inhibition of autophagy-regulated ferroptosis.
these results assign the TMEM189 gene to plasmanylethanolamine desaturase and suggest that the previously characterized phenotype of Tmem189-deficient mice may be caused by a lack of plasmalogens.
Title: The TMEM189 gene encodes plasmanylethanolamine desaturase which introduces the characteristic vinyl ether double bond into plasmalogens.
TMEM189 could functionally replace CarF in M. xanthus, and knockout of TMEM189 in a human cell line eliminated plasmalogens; study reveals TMEM189 as the long-sought desaturase for animal plasmalogen biosynthesis
Title: A bacterial light response reveals an orphan desaturase for human plasmalogen synthesis.
TMEM189 is a target gene of the BACH1 transcription factor according to ChIP-seq analysis in HEK 293 cells.
Title: The BTB and CNC homology 1 (BACH1) target genes are involved in the oxidative stress response and in control of the cell cycle.
Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Single nucleotide polymorphisms of matrix metalloproteinase 9 (MMP9) and tumor protein 73 (TP73) interact with Epstein-Barr virus in chronic lymphocytic leukemia: results from the European case-control study EpiLymph.

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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

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

D20S551E (e-PCR)
- UniSTS:28542

Kua__7422 (e-PCR)
- UniSTS:471476

RH63738 (e-PCR)
- UniSTS:31935

RH92983 (e-PCR)
- UniSTS:90818

Readthrough PEDS1-UBE2V1

Readthrough gene: PEDS1-UBE2V1, Included gene: UBE2V1

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables plasmanylethanolamine desaturase activity	IBA Inferred from Biological aspect of Ancestor more info
enables plasmanylethanolamine desaturase activity	IDA Inferred from Direct Assay more info	PubMed
enables plasmanylethanolamine desaturase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in ether lipid biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in ether lipid biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in ether lipid biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in fatty acid metabolic process	IEA Inferred from Electronic Annotation more info

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

General protein information

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Preferred Names: plasmanylethanolamine desaturase 1

Names: CarF homolog; transmembrane protein 189

NP_001155977.2

EC 1.14.99.19

NP_954580.2

EC 1.14.99.19

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_001162505.2 → NP_001155977.2 plasmanylethanolamine desaturase 1 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.

Source sequence(s)

AL034423

Consensus CDS

CCDS54473.1

Related

ENSP00000360713.5, ENST00000371650.9

Conserved Domains (1) summary

pfam10520
Location:85 → 258

TMEM189_B_dmain; B domain of TMEM189, localization domain
NM_199129.4 → NP_954580.2 plasmanylethanolamine desaturase 1 isoform 1

Status: REVIEWED

Description

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

Source sequence(s)

AL034423

Consensus CDS

CCDS13428.1

UniProtKB/Swiss-Prot

A5PLL7

Related

ENSP00000360715.4, ENST00000371652.9

Conserved Domains (1) summary

pfam10520
Location:85 → 261

TMEM189_B_dmain; B domain of TMEM189, localization domain

RNA

NR_027889.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) includes an additional internal exon, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AL034423