PEBP4

phosphatidylethanolamine binding protein 4

Basic information

Region (hg38): 8:22713250-23000000

Links

ENSG00000134020 ∙ NCBI:157310 ∙ OMIM:612473 ∙ HGNC:28319 ∙ Uniprot:Q96S96 ∙ 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 PEBP4 gene.

• Inborn genetic diseases (17 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PEBP4 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			16	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	0

Variants in PEBP4

This is a list of pathogenic ClinVar variants found in the PEBP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-22713405-T-G		not specified	Uncertain significance (Dec 27, 2023)
8-22713525-T-C		not specified	Uncertain significance (Jun 21, 2023)
8-22724845-C-T		not specified	Uncertain significance (May 04, 2022)
8-22724900-C-T		not specified	Uncertain significance (Feb 27, 2023)
8-22724903-A-G		not specified	Uncertain significance (Nov 15, 2021)
8-22724924-C-T		not specified	Uncertain significance (Jan 26, 2022)
8-22724948-C-G		not specified	Likely benign (Aug 17, 2021)
8-22727178-A-G		not specified	Uncertain significance (May 03, 2023)
8-22727190-C-G		not specified	Uncertain significance (Dec 13, 2022)
8-22727216-G-C		not specified	Uncertain significance (Feb 13, 2024)
8-22817687-C-T		not specified	Uncertain significance (May 17, 2023)
8-22920198-G-A		not specified	Uncertain significance (Jul 20, 2021)
8-22920209-A-G		not specified	Uncertain significance (Dec 14, 2023)
8-22920210-T-C		not specified	Uncertain significance (Jun 11, 2021)
8-22920231-T-A		not specified	Uncertain significance (Oct 29, 2021)
8-22920251-C-G		not specified	Uncertain significance (Aug 11, 2022)
8-22920252-A-G		not specified	Uncertain significance (May 27, 2022)
8-22927600-C-T		not specified	Uncertain significance (May 09, 2023)
8-22927629-G-T		not specified	Uncertain significance (Mar 03, 2022)
8-22927645-C-T		not specified	Uncertain significance (Jun 21, 2023)
8-22927689-G-A		not specified	Uncertain significance (Mar 27, 2023)
8-22994530-C-T			Benign (May 14, 2021)
8-22994558-C-T			Benign (Mar 01, 2022)
8-22994583-G-A		RHOBTB2-related disorder	Benign (Aug 18, 2020)
8-22994585-T-C			Uncertain significance (Jun 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PEBP4	protein_coding	protein_coding	ENST00000256404	6	286745

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000458	0.664	124752	0	46	124798	0.000184

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.666	150	129	1.17	0.00000666	1487
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000310	0.000310
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.0000564	0.0000556
Finnish	0.000279	0.000278
European (Non-Finnish)	0.000124	0.000124
Middle Eastern	0.0000564	0.0000556
South Asian	0.000523	0.000523
Other	0.000166	0.000165

dbNSFP

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

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.459

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.659

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pebp4

Gene ontology

• Cellular component: lysosome;extracellular exosome
• Molecular function: protein binding