PEAR1

platelet endothelial aggregation receptor 1

Basic information

Region (hg38): 1:156893697-156916429

Previous symbols: [ "MEGF12" ]

Links

ENSG00000187800 ∙ NCBI:375033 ∙ OMIM:610278 ∙ HGNC:33631 ∙ Uniprot:Q5VY43 ∙ 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 PEAR1 gene.

• Inborn genetic diseases (40 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PEAR1 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				1	2	3
missense			35	5	2	42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	6	4

Variants in PEAR1

This is a list of pathogenic ClinVar variants found in the PEAR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-156903934-C-T		not specified	Likely benign (Jan 03, 2022)
1-156903997-G-A		not specified	Likely benign (Sep 29, 2023)
1-156904816-G-A		not specified	Uncertain significance (Sep 25, 2023)
1-156904836-A-G		not specified	Uncertain significance (Dec 15, 2023)
1-156905337-A-G		not specified	Uncertain significance (Mar 01, 2024)
1-156905370-C-T		not specified	Uncertain significance (Nov 17, 2022)
1-156905392-A-G		not specified	Likely benign (Oct 22, 2021)
1-156905401-A-T		not specified	Uncertain significance (Dec 13, 2022)
1-156907615-A-G		not specified	Uncertain significance (Sep 16, 2021)
1-156907617-G-A		not specified	Uncertain significance (Sep 22, 2023)
1-156907710-A-C		not specified	Uncertain significance (Dec 06, 2022)
1-156907962-C-A		not specified	Uncertain significance (Jan 07, 2022)
1-156907990-G-T			Benign (May 08, 2018)
1-156908133-G-T		not specified	Uncertain significance (Dec 03, 2021)
1-156908163-A-G		not specified	Uncertain significance (Dec 28, 2022)
1-156908310-C-T		not specified	Uncertain significance (Nov 18, 2022)
1-156908334-G-A		not specified	Uncertain significance (Aug 12, 2022)
1-156908735-C-T		not specified	Uncertain significance (Feb 28, 2024)
1-156908754-G-A			Likely benign (Jan 01, 2023)
1-156908792-C-A		not specified	Uncertain significance (Oct 03, 2022)
1-156908997-G-T		not specified	Uncertain significance (Dec 07, 2021)
1-156909760-G-C		not specified	Uncertain significance (Jan 03, 2022)
1-156909831-C-T		not specified	Uncertain significance (Dec 21, 2022)
1-156909837-G-A		not specified	Uncertain significance (May 23, 2023)
1-156909841-T-C		not specified	Likely benign (Feb 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PEAR1	protein_coding	protein_coding	ENST00000338302	22	22737

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.48e-20	0.821	125647	0	101	125748	0.000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.712	595	646	0.921	0.0000391	6697
Missense in Polyphen		179	213.75	0.83743		2278
Synonymous	-0.297	255	249	1.02	0.0000155	1991
Loss of Function	2.26	40	58.7	0.682	0.00000303	614

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000544	0.000544
Ashkenazi Jewish	0.000202	0.000198
East Asian	0.00118	0.00114
Finnish	0.000188	0.000185
European (Non-Finnish)	0.000369	0.000360
Middle Eastern	0.00118	0.00114
South Asian	0.000564	0.000555
Other	0.000669	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: When overexpressed, reduces the number of both early and late non-adherent myeloid progenitor cells. {ECO:0000250}.

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.208
• rvis_EVS: 0.68
• rvis_percentile_EVS: 84.77

Haploinsufficiency Scores

• pHI: 0.138
• hipred: N
• hipred_score: 0.329
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.104

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pear1
• Phenotype: hematopoietic system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: phosphatidylinositol 3-kinase signaling;protein kinase B signaling;recognition of apoptotic cell;negative regulation of Notch signaling pathway;platelet aggregation
• Cellular component: phagocytic cup;integral component of membrane
• Molecular function: signaling receptor activity