PEBP1

phosphatidylethanolamine binding protein 1

Basic information

Region (hg38): 12:118136124-118145584

Previous symbols: [ "PBP" ]

Links

ENSG00000089220 ∙ NCBI:5037 ∙ OMIM:604591 ∙ HGNC:8630 ∙ Uniprot:P30086 ∙ 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 PEBP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PEBP1 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			4	1	2	7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	1	2

Variants in PEBP1

This is a list of pathogenic ClinVar variants found in the PEBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-118136238-G-C		not specified	Uncertain significance (Mar 11, 2024)
12-118136289-T-C		not specified	Uncertain significance (Jun 03, 2022)
12-118138115-C-T		not specified	Uncertain significance (Aug 02, 2022)
12-118139489-A-G			Benign (May 21, 2018)
12-118144628-C-T		not specified	Uncertain significance (Jan 24, 2024)
12-118144672-C-T			Benign (Dec 31, 2019)
12-118144720-A-G		not specified	Likely benign (May 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PEBP1	protein_coding	protein_coding	ENST00000261313	4	9727

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0917	0.873	125713	0	35	125748	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.942	83	111	0.748	0.00000638	1202
Missense in Polyphen		20	26.198	0.76341		278
Synonymous	-0.127	53	51.8	1.02	0.00000348	371
Loss of Function	1.80	3	8.75	0.343	4.57e-7	94

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000266	0.000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds ATP, opioids and phosphatidylethanolamine. Has lower affinity for phosphatidylinositol and phosphatidylcholine. Serine protease inhibitor which inhibits thrombin, neuropsin and chymotrypsin but not trypsin, tissue type plasminogen activator and elastase (By similarity). Inhibits the kinase activity of RAF1 by inhibiting its activation and by dissociating the RAF1/MEK complex and acting as a competitive inhibitor of MEK phosphorylation. {ECO:0000250, ECO:0000269|PubMed:18294816}.
• Pathway: EGF-Ncore;EGF-EGFR Signaling Pathway;MAP2K and MAPK activation;Disease;Signal Transduction;signal transduction through il1r;EGFR1;ErbB1 downstream signaling;Negative regulation of MAPK pathway;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;Signaling by RAS mutants;Signaling by high-kinase activity BRAF mutants;Signaling by moderate kinase activity BRAF mutants;Paradoxical activation of RAF signaling by kinase inactive BRAF;Aurora B signaling;Signaling by BRAF and RAF fusions;Oncogenic MAPK signaling;Diseases of signal transduction (Consensus)

Recessive Scores

• pRec: 0.284

Intolerance Scores

• loftool: 0.554
• rvis_EVS: 0.35
• rvis_percentile_EVS: 73.97

Haploinsufficiency Scores

• pHI: 0.0688
• hipred: Y
• hipred_score: 0.835
• ghis: 0.413

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.988

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pebp1
• Phenotype: taste/olfaction phenotype

Gene ontology

• Biological process: MAPK cascade;regulation of neurotransmitter levels;regulation of the force of heart contraction;response to oxidative stress;aging;response to heat;response to wounding;response to toxic substance;response to organonitrogen compound;negative regulation of endopeptidase activity;response to activity;hippocampus development;negative regulation of MAPK cascade;positive regulation of cAMP-mediated signaling;response to ethanol;positive regulation of mitotic nuclear division;sperm capacitation;response to corticosterone;response to cAMP;response to calcium ion;positive regulation of acetylcholine metabolic process
• Cellular component: extracellular space;nucleus;mitochondrion;mitochondrial outer membrane;Golgi apparatus;cytosol;synaptic vesicle;cell surface;neuronal cell body;myelin sheath;axon terminus;apical part of cell;extracellular exosome
• Molecular function: RNA binding;serine-type endopeptidase inhibitor activity;signaling receptor binding;protein binding;ATP binding;phosphatidylethanolamine binding;enzyme binding;protein kinase binding;mitogen-activated protein kinase binding