PEBP4

protein-coding

phosphatidylethanolamine binding protein 4

Gene summary

The phosphatidylethanolamine (PE)-binding proteins, including PEBP4, are an evolutionarily conserved family of proteins with pivotal biologic functions, such as lipid binding and inhibition of serine proteases (Wang et al., 2004 [PubMed 15302887]).[supplied by OMIM, Dec 2008]

MANE transcript

NM_144962.3

Inheritance

—

ClinVar variants

U:55B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.71

Max pathogenic AF

—

Genomic locus

chr8:22,713,251-23,000,000

External References & Databases

Ensembl (ENSG00000134020)

Transcript & Mutation Effects

hg38 • Region Span ~286.7 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 PEBP4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 57

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_144962.3. 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			54 clinvar	4 clinvar		58
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	55	4	0	59

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_144962.3	RefSeq	NP_659399.2	6	MANE Select
ENST00000256404.8	Ensembl	ENSP00000256404.6	6	MANE Select
NM_001363233.2	RefSeq	NP_001350162.1	6	Standard
ENST00000522278.1	Ensembl	ENSP00000429414.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

lysosome
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000256404
Coding exons: 6
Length: 286745
Individuals with no LoFs: 124752
Homozygous LoFs: 0
Heterozygous LoFs: 46
Defined: 124798
p: 0.000184

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.666	150	129	1.17	0.00000666	1487
Missense (PolyPhen)		43	35.216	1.221		405
Synonymous	-0.628	54	48.4	1.11	0.00000286	410
Loss of Function	0.887	8	11.2	0.714	5.74e-7	121

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00019	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000056	0.000056	rare
Finnish	0.00028	0.00028	rare
European (Non-Finnish)	0.00012	0.00012	rare
South Asian	0.00052	0.00052	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Seems to promote cellular resistance to TNF-induced apoptosis by inhibiting activation of the Raf-1/MEK/ERK pathway, JNK and phosphatidylethanolamine externalization. {ECO:0000269|PubMed:15302887}.;

Intolerance Scores

LoFtool: 0.745
RVIS EVS: 0.97
RVIS percentile EVS: 90.34

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.659

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	Medium	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High