PEDS1

plasmanylethanolamine desaturase 1

Basic information

Region (hg38): 20:50118253-50153734

Previous symbols: [ "TMEM189" ]

Links

ENSG00000240849

∙ NCBI:387521 ∙ OMIM:610994 ∙ HGNC:16735 ∙ Uniprot:A5PLL7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PEDS1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PEDS1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			2 clinvar			2
nonsense						0
start loss						0
frameshift			1 clinvar			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in PEDS1

This is a list of pathogenic ClinVar variants found in the PEDS1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Phenotype	Significance	ClinVar
20-50125110-G-A	not specified	Uncertain significance (Jun 02, 2023)	2524882
20-50125137-C-T	not specified	Uncertain significance (Jul 06, 2021)	3211321
20-50153533-AG-A	See cases	Uncertain significance (-)	3233344

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PEDS1	protein_coding	protein_coding	ENST00000557021	8	72673

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00839	0.989	125665	0	8	125673	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.43	112	211	0.530	0.0000124	2374
Missense in Polyphen		27	66.263	0.40747		630
Synonymous	-1.18	95	81.4	1.17	0.00000490	713
Loss of Function	2.65	7	19.7	0.356	0.00000110	203

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000887	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

Pathway: TLR NFkB;Toll Like Receptor 7/8 (TLR7/8) Cascade;Interleukin-17 signaling;Signaling by Interleukins;TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling;Cytokine Signaling in Immune system;Toll Like Receptor 9 (TLR9) Cascade;MyD88 cascade initiated on plasma membrane;Toll Like Receptor 10 (TLR10) Cascade;TICAM1, RIP1-mediated IKK complex recruitment ;Toll Like Receptor 3 (TLR3) Cascade;Toll Like Receptor 5 (TLR5) Cascade;B cell receptor signaling;Toll-Like Receptors Cascades;Downstream TCR signaling;TCR signaling;NOD1/2 Signaling Pathway;Nucleotide-binding domain, leucine rich repeat containing receptor (NLR) signaling pathways;protein ubiquitylation;Interleukin-1 signaling;IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation;Innate Immune System;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;IL-1 NFkB;Class I MHC mediated antigen processing & presentation;IL-1 p38;IL-1 JNK;IL1;TLR p38;TAK1 activates NFkB by phosphorylation and activation of IKKs complex;JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1;activated TAK1 mediates p38 MAPK activation;MAP kinase activation;TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation;MyD88 dependent cascade initiated on endosome;TLR JNK;IKK complex recruitment mediated by RIP1;TRIF(TICAM1)-mediated TLR4 signaling ;MyD88-independent TLR4 cascade ;Toll Like Receptor 4 (TLR4) Cascade;IRAK1 recruits IKK complex;MyD88:Mal cascade initiated on plasma membrane;Toll Like Receptor TLR1:TLR2 Cascade;Toll Like Receptor TLR6:TLR2 Cascade;Toll Like Receptor 2 (TLR2) Cascade;IL1-mediated signaling events;Interleukin-1 family signaling;CD4 T cell receptor signaling-NFkB cascade;CD4 T cell receptor signaling (Consensus)

Recessive Scores

pRec: 0.139

Intolerance Scores

loftool: 0.591
rvis_EVS: -0.43
rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

pHI
hipred: Y
hipred_score: 0.508
ghis: 0.518

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: K
gene_indispensability_pred: E
gene_indispensability_score: 0.731

Mouse Genome Informatics

Gene name: Tmem189
Phenotype: hematopoietic system phenotype; skeleton phenotype; immune system phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype; craniofacial phenotype;

Gene ontology

Biological process
Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane
Molecular function