PEDS1

gene
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Also known as Kua

Summary

PEDS1 (plasmanylethanolamine desaturase 1, HGNC:16735) is a protein-coding gene on chromosome 20q13.13, encoding Plasmanylethanolamine desaturase 1 (A5PLL7). Plasmanylethanolamine desaturase involved in plasmalogen biogenesis in the endoplasmic reticulum membrane.

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.

Source: NCBI Gene 387521 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 8 total
  • MANE Select transcript: NM_199129

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16735
Approved symbolPEDS1
Nameplasmanylethanolamine desaturase 1
Location20q13.13
Locus typegene with protein product
StatusApproved
AliasesKua
Ensembl geneENSG00000240849
Ensembl biotypeprotein_coding
OMIM610994
Entrez387521

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 10 protein_coding, 2 nonsense_mediated_decay

ENST00000371650, ENST00000371652, ENST00000371656, ENST00000371658, ENST00000453505, ENST00000879855, ENST00000879856, ENST00000879857, ENST00000879858, ENST00000879859, ENST00000879860, ENST00000879861

RefSeq mRNA: 2 — MANE Select: NM_199129 NM_001162505, NM_199129

CCDS: CCDS13428, CCDS54473

Canonical transcript exons

ENST00000371652 — 6 exons

ExonStartEnd
ENSE000035227965012797550128187
ENSE000035975885014350250143621
ENSE000036280605012954650129690
ENSE000036946675013085650130947
ENSE000037303835011825450125179
ENSE000038473385015351750153723

Expression profiles

Bgee: expression breadth ubiquitous, 234 present calls, max score 95.72.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 25.0576 / max 174.6032, expressed in 1803 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
18782824.71951803
18782921.37031810
1878230.3381135

Top tissues by expression

249 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
lower esophagus mucosaUBERON:003583495.72gold quality
C1 segment of cervical spinal cordUBERON:000646995.43gold quality
spinal cordUBERON:000224094.91gold quality
upper arm skinUBERON:000426394.11gold quality
stromal cell of endometriumCL:000225593.46gold quality
esophagus mucosaUBERON:000246993.20gold quality
skin of legUBERON:000151193.10gold quality
skin of abdomenUBERON:000141692.97gold quality
esophagusUBERON:000104391.38gold quality
zone of skinUBERON:000001491.32gold quality
olfactory segment of nasal mucosaUBERON:000538690.98gold quality
muscle layer of sigmoid colonUBERON:003580590.91gold quality
inferior vagus X ganglionUBERON:000536390.22gold quality
gastrocnemiusUBERON:000138890.11gold quality
upper lobe of left lungUBERON:000895290.07gold quality
esophagogastric junction muscularis propriaUBERON:003584189.96gold quality
tibial nerveUBERON:000132389.78gold quality
smooth muscle tissueUBERON:000113589.67gold quality
lower esophagusUBERON:001347389.44gold quality
lower esophagus muscularis layerUBERON:003583389.40gold quality
apex of heartUBERON:000209889.34gold quality
substantia nigraUBERON:000203889.30gold quality
vaginaUBERON:000099689.29gold quality
mucosa of transverse colonUBERON:000499189.09gold quality
upper lobe of lungUBERON:000894889.07gold quality
muscle of legUBERON:000138388.92gold quality
ectocervixUBERON:001224988.79gold quality
midbrainUBERON:000189188.76gold quality
left coronary arteryUBERON:000162688.70gold quality
putamenUBERON:000187488.70gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-MTAB-7303no370.27
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

61 targeting PEDS1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-656-3P100.0072.152788
HSA-MIR-3646100.0073.565283
HSA-MIR-340-5P100.0072.504437
HSA-MIR-126-5P100.0072.713180
HSA-MIR-4481100.0066.421669
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-314899.9775.066478
HSA-MIR-426799.9666.532368
HSA-MIR-185-3P99.9567.011743
HSA-MIR-96-5P99.9572.802140
HSA-MIR-1213399.9271.822006
HSA-MIR-568099.9169.833421
HSA-MIR-129799.9173.413162
HSA-MIR-1271-5P99.9171.991972
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-182-5P99.8774.032589
HSA-MIR-6756-5P99.8267.972466
HSA-MIR-471999.7372.103329
HSA-MIR-4699-3P99.7170.153142
HSA-MIR-6766-5P99.6867.702325
HSA-MIR-6887-3P99.6667.831778
HSA-MIR-1249-5P99.6166.552049
HSA-MIR-6797-5P99.6166.552084
HSA-MIR-613299.6065.831554
HSA-MIR-6836-5P99.6065.621538
HSA-MIR-426199.5970.303415
HSA-MIR-608199.4866.071446
HSA-MIR-127599.4767.902749
HSA-MIR-6722-3P99.4567.621919
HSA-MIR-128-1-5P99.3360.46332

Literature-anchored findings (GeneRIF, showing 4)

  • TMEM189 is a target gene of the BACH1 transcription factor according to ChIP-seq analysis in HEK 293 cells. (PMID:21555518)
  • 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 (PMID:31604315)
  • 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. (PMID:32209662)
  • TMEM189 promotes breast cancer through inhibition of autophagy-regulated ferroptosis. (PMID:35843092)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusPeds1ENSMUSG00000090213
rattus_norvegicusUbe2v1ENSRNOG00000025580

Paralogs (24): UBE2T (ENSG00000077152), UBE2A (ENSG00000077721), UBE2K (ENSG00000078140), CDC34 (ENSG00000099804), UBE2I (ENSG00000103275), UBE2W (ENSG00000104343), UBE2R2 (ENSG00000107341), UBE2S (ENSG00000108106), UBE2B (ENSG00000119048), UBE2G1 (ENSG00000132388), UBE2Z (ENSG00000159202), UBE2J2 (ENSG00000160087), AKTIP (ENSG00000166971), UBE2V2 (ENSG00000169139), UBE2C (ENSG00000175063), UBE2O (ENSG00000175931), UBE2U (ENSG00000177414), UBE2N (ENSG00000177889), UBE2F (ENSG00000184182), UBE2G2 (ENSG00000184787), UBE2H (ENSG00000186591), UBE2J1 (ENSG00000198833), UBE2V1 (ENSG00000244687), UBE2NL (ENSG00000276380)

Protein

Protein identifiers

Plasmanylethanolamine desaturase 1A5PLL7 (reviewed: A5PLL7)

Alternative names: Transmembrane protein 189

All UniProt accessions (4): A5PLL7, F8W924, F8WBY2, Q5TGE2

UniProt curated annotations — full annotation on UniProt →

Function. Plasmanylethanolamine desaturase involved in plasmalogen biogenesis in the endoplasmic reticulum membrane. Plasmalogens are glycerophospholipids with a hydrocarbon chain linked by a vinyl ether bond at the glycerol sn-1 position, and are involved in antioxidative and signaling mechanisms.

Subcellular location. Endoplasmic reticulum membrane.

Domain organisation. Histidine box-1 and -2 together with other histidine residues are essential for catalytic activity.

Pathway. Lipid metabolism; fatty acid metabolism.

Miscellaneous. In human, PEDS1 and UBE2V1 are adjacent genes which can produce independent proteins and can also be fused to form a PEDS1-UBE2V1 hybrid protein.

Similarity. Belongs to the fatty acid desaturase CarF family.

Isoforms (2)

UniProt IDNamesCanonical?
A5PLL7-11yes
A5PLL7-22

RefSeq proteins (2): NP_001155977, NP_954580* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR019547Lipid_desatDomain
IPR052601Plasmalogen_desaturaseFamily

Pfam: PF10520

Enzyme classification (BRENDA):

  • EC 1.14.19.77 — plasmanylethanolamine desaturase (BRENDA: 6 organisms, 22 substrates, 11 inhibitors, 0 Km, 0 kcat entries)

Catalyzed reactions (Rhea), 4 shown:

  • a 1-(1,2-saturated alkyl)-2-acyl-sn-glycero-3-phosphoethanolamine + 2 Fe(II)-[cytochrome b5] + O2 + 2 H(+) = a 1-O-(1Z-alkenyl)-2-acyl-sn-glycero-3-phosphoethanolamine + 2 Fe(III)-[cytochrome b5] + 2 H2O (RHEA:22956)
  • a 1-O-hexadecyl-2-acyl-sn-glycero-3-phosphoethanolamine + 2 Fe(II)-[cytochrome b5] + O2 + 2 H(+) = a 1-O-(1Z-hexadecenyl)-2-acyl-sn-glycero-3-phosphoethanolamine + 2 Fe(III)-[cytochrome b5] + 2 H2O (RHEA:61960)
  • a 1-O-octadecyl-2-acyl-sn-glycero-3-phosphoethanolamine + 2 Fe(II)-[cytochrome b5] + O2 + 2 H(+) = a 1-O-(1Z-octadecenyl)-2-acyl-sn-glycero-3-phosphoethanolamine + 2 Fe(III)-[cytochrome b5] + 2 H2O (RHEA:61964)
  • a 1-O-(9Z-octadecenyl)-2-acyl-sn-glycero-3-phosphoethanolamine + 2 Fe(II)-[cytochrome b5] + O2 + 2 H(+) = a 1-O-(1Z,9Z-octadecadienyl)-2-acyl-sn-glycero-3-phosphoethanolamine + 2 Fe(III)-[cytochrome b5] + 2 H2O (RHEA:61968)

UniProt features (31 total): mutagenesis site 12, site 8, transmembrane region 3, sequence conflict 3, short sequence motif 2, chain 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-A5PLL7-F190.820.74

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (8): 190 (essential for catalytic activity); 214 (essential for catalytic activity); 217 (essential for catalytic activity); 218 (essential for catalytic activity); 95 (essential for catalytic activity); 120 (essential for catalytic activity); 121 (essential for catalytic activity); 186 (essential for catalytic activity)

Mutagenesis-validated functional residues (12):

PositionPhenotype
95loss of plasmanylethanolamine desaturase activity.
120loss of plasmanylethanolamine desaturase activity.
121loss of plasmanylethanolamine desaturase activity.
130loss of plasmanylethanolamine desaturase activity.
186loss of plasmanylethanolamine desaturase activity.
190loss of plasmanylethanolamine desaturase activity.
206no effect on plasmanylethanolamine desaturase activity.
213no effect on plasmanylethanolamine desaturase activity.
214loss of plasmanylethanolamine desaturase activity.
217loss of plasmanylethanolamine desaturase activity.
218loss of plasmanylethanolamine desaturase activity.
222no effect on desaturase plasmanylethanolamine activity.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 112 (showing top): GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_PAIRED_DONORS_WITH_INCORPORATION_OR_REDUCTION_OF_MOLECULAR_OXYGEN, AAGCCAT_MIR135A_MIR135B, GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS, FOSTER_TOLERANT_MACROPHAGE_DN, GOBP_LIPID_METABOLIC_PROCESS, GOBP_ORGANIC_ACID_METABOLIC_PROCESS, GOBP_LIPID_BIOSYNTHETIC_PROCESS, VANTVEER_BREAST_CANCER_ESR1_DN, GOCC_NUCLEAR_OUTER_MEMBRANE_ENDOPLASMIC_RETICULUM_MEMBRANE_NETWORK, GOBP_FATTY_ACID_METABOLIC_PROCESS, GOCC_ORGANELLE_SUBCOMPARTMENT, NIKOLSKY_BREAST_CANCER_20Q12_Q13_AMPLICON, CHEN_METABOLIC_SYNDROM_NETWORK, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, KASLER_HDAC7_TARGETS_1_UP

GO Biological Process (3): fatty acid metabolic process (GO:0006631), ether lipid biosynthetic process (GO:0008611), lipid metabolic process (GO:0006629)

GO Molecular Function (3): plasmanylethanolamine desaturase activity (GO:0050207), protein binding (GO:0005515), oxidoreductase activity (GO:0016491)

GO Cellular Component (3): endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
lipid metabolic process1
monocarboxylic acid metabolic process1
lipid biosynthetic process1
ether lipid metabolic process1
glycerol ether biosynthetic process1
primary metabolic process1
oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water1
binding1
catalytic activity1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
cellular anatomical structure1

Protein interactions and networks

STRING

810 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PEDS1G3V2F7G3V2F7864
PEDS1UBBP02248731
PEDS1UBBP02248726
PEDS1PDCLQ13371714
PEDS1GHITMQ9H3K2596
PEDS1COPS7AQ9UBW8583
PEDS1UBE2D2P51669574
PEDS1AGPSO00116572
PEDS1UBE2V2Q15819548
PEDS1LALBAP00709540
PEDS1UBE2KP27924530
PEDS1FAR1Q8WVX9510
PEDS1GNPATO15228506
PEDS1UBE2IP50550463
PEDS1UBE2D1P51668462

IntAct

12 interactions, top by confidence:

ABTypeScore
LAMP2PEDS1psi-mi:“MI:0915”(physical association)0.560
SH3GLB1PEDS1psi-mi:“MI:0915”(physical association)0.560
PEDS1psi-mi:“MI:0915”(physical association)0.370
CHRNA4TMEM223psi-mi:“MI:0914”(association)0.350
NCR3LG1PEDS1psi-mi:“MI:0914”(association)0.350
RHBGPEDS1psi-mi:“MI:0914”(association)0.350
TCTN3TMEM120Bpsi-mi:“MI:2364”(proximity)0.270

BioGRID (87): UBC (Reconstituted Complex), CHORDC1 (Co-fractionation), RAB7A (Co-fractionation), TAGLN2 (Co-fractionation), UBE2K (Co-fractionation), UBE2N (Co-fractionation), TMEM189-UBE2V1 (Co-fractionation), TMEM189-UBE2V1 (Co-fractionation), TMEM189-UBE2V1 (Co-fractionation), TMEM189-UBE2V1 (Co-fractionation), TMEM189-UBE2V1 (Co-fractionation), TMEM189-UBE2V1 (Co-fractionation), TMEM189-UBE2V1 (Co-fractionation), TMEM189-UBE2V1 (Proximity Label-MS), TMEM189 (Affinity Capture-MS)

ESM2 similar proteins: A2VE61, A5PLL7, A6QLM0, B1AZA5, B8BIM2, D3ZXD8, E9PTA2, O35052, O75907, O94759, P48631, P52848, P98191, Q02353, Q05B45, Q0P5C0, Q0VCJ8, Q2QZ14, Q3UHN9, Q4R4U1, Q4R766, Q5EA70, Q5HZE2, Q5R5F8, Q5R7B1, Q61115, Q6DD32, Q6NYY9, Q6P360, Q6PHN7, Q84VT2, Q8BFQ2, Q8C1E7, Q8GZC3, Q8MK44, Q8NBD8, Q8NBT3, Q8VWZ8, Q90693, Q91YD4

Diamond homologs: A5PLL7, A6QLM0, Q5UR78, Q99LQ7, Q9AE87, Q9SZ42, O81006, O04584

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

8 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance6
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1052 predictions. Top by Δscore:

VariantEffectΔscore
20:50127969:CCGCA:Cdonor_loss1.0000
20:50127970:CGCA:Cdonor_loss1.0000
20:50127970:CGCAC:Cdonor_loss1.0000
20:50127971:GCA:Gdonor_loss1.0000
20:50127971:GCACC:Gdonor_loss1.0000
20:50127972:CAC:Cdonor_loss1.0000
20:50127973:AC:Adonor_loss1.0000
20:50127974:C:CGdonor_loss1.0000
20:50129541:CTCA:Cdonor_loss1.0000
20:50129543:CA:Cdonor_loss1.0000
20:50129544:A:ACdonor_gain1.0000
20:50129545:C:Adonor_loss1.0000
20:50129545:C:CCdonor_gain1.0000
20:50129545:C:CGdonor_loss1.0000
20:50129689:GCC:Gacceptor_loss1.0000
20:50129691:C:CAacceptor_loss1.0000
20:50129692:T:Gacceptor_loss1.0000
20:50129697:T:Cacceptor_gain1.0000
20:50129697:T:TCacceptor_gain1.0000
20:50143500:A:ACdonor_gain1.0000
20:50143501:C:CCdonor_gain1.0000
20:50143501:CCAA:Cdonor_gain1.0000
20:50153511:TCTTA:Tdonor_loss1.0000
20:50153512:CTTA:Cdonor_loss1.0000
20:50153513:TTA:Tdonor_loss1.0000
20:50153513:TTAC:Tdonor_loss1.0000
20:50153514:TA:Tdonor_loss1.0000
20:50153515:ACC:Adonor_loss1.0000
20:50153516:C:CAdonor_loss1.0000
20:50128185:CTT:Cacceptor_gain0.9900

AlphaMissense

1760 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
20:50128017:G:CH217D1.000
20:50125169:G:CN234K0.999
20:50125169:G:TN234K0.999
20:50127985:G:CC227W0.999
20:50127986:C:TC227Y0.999
20:50127988:G:CF226L0.999
20:50127988:G:TF226L0.999
20:50127990:A:GF226L0.999
20:50128012:G:CH218Q0.999
20:50128012:G:TH218Q0.999
20:50128014:G:CH218D0.999
20:50128015:G:CH217Q0.999
20:50128015:G:TH217Q0.999
20:50128017:G:TH217N0.999
20:50128026:G:CH214D0.999
20:50128026:G:TH214N0.999
20:50128096:G:CH190Q0.999
20:50128096:G:TH190Q0.999
20:50128098:G:CH190D0.999
20:50128110:G:CH186D0.999
20:50128117:G:CN183K0.999
20:50128117:G:TN183K0.999
20:50129638:C:GR129P0.999
20:50129661:G:CH121Q0.999
20:50129661:G:TH121Q0.999
20:50129663:G:CH121D0.999
20:50129664:G:CH120Q0.999
20:50129664:G:TH120Q0.999
20:50129666:G:CH120D0.999
20:50129666:G:TH120N0.999

dbSNP variants (sampled 300 via entrez): RS1000070167 (20:50151211 C>A,T), RS1000101479 (20:50144441 A>G), RS1000149984 (20:50121955 C>G,T), RS1000174731 (20:50117944 G>A), RS1000223296 (20:50143436 C>T), RS1000229490 (20:50121554 TAAG>T), RS1000283527 (20:50121825 T>C), RS1000307000 (20:50127840 A>T), RS1000336555 (20:50155040 G>A,C), RS1000351762 (20:50149033 A>T), RS1000407317 (20:50149318 C>T), RS1000460333 (20:50155660 C>G), RS1000502451 (20:50122204 G>C), RS1000548095 (20:50139928 AC>A), RS1000629907 (20:50145185 G>A,C)

Disease associations

OMIM: gene MIM:610994 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

StudyTraitp-value
GCST004608_113Granulocyte percentage of myeloid white cells3.000000e-16
GCST004609_161Monocyte percentage of white cells1.000000e-18

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0007997granulocyte percentage of myeloid white cells
EFO:0007989monocyte percentage of leukocytes

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases expression2
aristolochic acid Iincreases expression1
ginger extractdecreases expression, increases abundance1
methylmercuric chlorideincreases expression1
bisphenol Adecreases methylation1
trichostatin Aaffects expression1
perfluorooctane sulfonic aciddecreases expression1
CGP 52608affects binding, increases reaction1
abrinedecreases expression1
Arsenicaffects methylation1
Benzo(a)pyrenedecreases methylation1
Diazinonincreases methylation1
Estradiolincreases expression1
Oils, Volatiledecreases expression, increases abundance1
Smokedecreases expression1
Thimerosaldecreases expression1
Tobacco Smoke Pollutionincreases expression1
Cyclosporineincreases expression1
Okadaic Acidincreases expression1
Particulate Matterincreases expression1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B5L1HAP1 TMEM189 (-) 2Cancer cell lineMale
CVCL_B5L2HAP1 TMEM189 (-) 3Cancer cell lineMale
CVCL_XU44HAP1 TMEM189 (-) 1Cancer cell lineMale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.