ADGRE1

adhesion G protein-coupled receptor E1, the group of Adhesion G protein-coupled receptors, subfamily E

Basic information

Region (hg38): 19:6887565-6940459

Previous symbols: [ "TM7LN3", "EMR1" ]

Links

ENSG00000174837 ∙ NCBI:2015 ∙ OMIM:600493 ∙ HGNC:3336 ∙ Uniprot:Q14246 ∙ 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 ADGRE1 gene.

• Inborn genetic diseases (39 variants)
• not provided (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADGRE1 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	1	2
missense			37	2	4	43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	37	3	6

Variants in ADGRE1

This is a list of pathogenic ClinVar variants found in the ADGRE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-6887613-G-T			Benign (Apr 30, 2018)
19-6890520-C-T		not specified	Uncertain significance (Sep 20, 2023)
19-6896467-A-G		not specified	Uncertain significance (Jul 26, 2022)
19-6896473-C-T		not specified	Uncertain significance (Jan 03, 2022)
19-6897184-G-C			Benign (Apr 10, 2018)
19-6897284-C-T		not specified	Uncertain significance (May 26, 2023)
19-6897294-C-A		not specified	Uncertain significance (Apr 20, 2023)
19-6897448-A-G		not specified	Likely benign (Aug 02, 2021)
19-6897454-G-A		not specified	Uncertain significance (Jun 18, 2021)
19-6897482-A-C		not specified	Uncertain significance (Oct 10, 2023)
19-6897500-G-A		not specified	Likely benign (May 26, 2022)
19-6897507-C-A		not specified	Uncertain significance (Oct 25, 2022)
19-6897542-G-C		not specified	Uncertain significance (Sep 22, 2023)
19-6901893-A-G		not specified	Uncertain significance (Feb 15, 2023)
19-6901977-G-T		not specified	Uncertain significance (Nov 03, 2023)
19-6903840-T-A		not specified	Uncertain significance (Jan 07, 2022)
19-6903912-G-A		not specified	Uncertain significance (Sep 29, 2023)
19-6903946-T-G		not specified	Uncertain significance (Feb 23, 2023)
19-6904087-G-T		not specified	Uncertain significance (Oct 17, 2023)
19-6904128-G-A		not specified	Uncertain significance (Feb 28, 2024)
19-6904137-C-A		not specified	Uncertain significance (Apr 07, 2022)
19-6906444-A-G		not specified	Uncertain significance (Jan 23, 2023)
19-6906458-T-C			Benign (Feb 01, 2024)
19-6906462-A-T		not specified	Uncertain significance (Jul 12, 2023)
19-6906486-C-A		not specified	Uncertain significance (Dec 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ADGRE1	protein_coding	protein_coding	ENST00000312053	21	52894

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.48e-23	0.00884	125541	0	206	125747	0.000819

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.515	452	484	0.934	0.0000249	5862
Missense in Polyphen		134	150.98	0.88755		1987
Synonymous	0.232	185	189	0.979	0.0000108	1660
Loss of Function	0.906	39	45.6	0.855	0.00000223	542

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00223	0.00223
Ashkenazi Jewish	0.00179	0.00159
East Asian	0.000490	0.000489
Finnish	0.0000938	0.0000924
European (Non-Finnish)	0.000358	0.000352
Middle Eastern	0.000490	0.000489
South Asian	0.00258	0.00258
Other	0.00108	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Orphan receptor involved in cell adhesion and probably in cell-cell interactions specifically involving cells of the immune system. May play a role in regulatory T-cells (Treg) development. {ECO:0000250|UniProtKB:Q61549}.
• Pathway: GPCRs, Class B Secretin-like;Signaling by GPCR;Signal Transduction;Class B/2 (Secretin family receptors);GPCR ligand binding (Consensus)

Recessive Scores

• pRec: 0.0904

Intolerance Scores

• rvis_EVS: 2.74
• rvis_percentile_EVS: 98.97

Haploinsufficiency Scores

• pHI: 0.0612
• hipred: N
• hipred_score: 0.123
• ghis: 0.387

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Adgre1
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: adaptive immune response;cell adhesion;cell surface receptor signaling pathway;G protein-coupled receptor signaling pathway;adenylate cyclase-activating G protein-coupled receptor signaling pathway
• Cellular component: integral component of plasma membrane;external side of plasma membrane
• Molecular function: G protein-coupled receptor activity;calcium ion binding