PEDS1

protein-coding

plasmanylethanolamine desaturase 1

Gene 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]

Previous symbols:

TMEM189

MANE transcript

NM_199129.4

Inheritance

—

ClinVar variants

U:7B:1

Top phenotype

See cases

gnomAD constraint

pLI —, LoF o/e 0.36

Max pathogenic AF

—

Genomic locus

chr20:50,118,254-50,153,734

External References & Databases

Ensembl (ENSG00000240849)

Transcript & Mutation Effects

hg38 • Region Span ~35.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PEDS1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 7

not providedTotal: 1

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_199129.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			6 clinvar	1 clinvar		7
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	7	1	0	8

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_199129.4	RefSeq	NP_954580.2	6	MANE Select
ENST00000371652.9	Ensembl	ENSP00000360715.4	6	MANE Select
NM_001162505.2	RefSeq	NP_001155977.2	6	Standard
ENST00000371650.10	Ensembl	ENSP00000360713.5	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Cellular Component

endoplasmic reticulum
endoplasmic reticulum membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000557021
Coding exons: 8
Length: 72673
Individuals with no LoFs: 125665
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 125673
p: 0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.43	112	211	0.530	0.0000124	2374
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000089	0.0000088	rare
South Asian	0.000098	0.000098	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.139

Intolerance Scores

LoFtool: 0.591
RVIS EVS: -0.43
RVIS percentile EVS: 25.15

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): K
Indispensability pred.: E
Indispensability score: 0.731