ADGRA2

adhesion G protein-coupled receptor A2, the group of Immunoglobulin like domain containing|Adhesion G protein-coupled receptors, subfamily A

Basic information

Region (hg38): 8:37784190-37844896

Previous symbols: [ "GPR124" ]

Links

ENSG00000020181 ∙ NCBI:25960 ∙ OMIM:606823 ∙ HGNC:17849 ∙ Uniprot:Q96PE1 ∙ 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 ADGRA2 gene.

• Inborn genetic diseases (88 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADGRA2 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
missense			71	1	3	75
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			16			16
Total	0	0	87	1	4

Variants in ADGRA2

This is a list of pathogenic ClinVar variants found in the ADGRA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-37784262-C-G			Likely benign (Apr 01, 2023)
8-37797308-C-A		not specified	Uncertain significance (Jul 14, 2022)
8-37797356-G-A		not specified	Uncertain significance (Dec 15, 2022)
8-37797368-G-T		not specified	Likely benign (Aug 03, 2022)
8-37797437-G-C		not specified	Uncertain significance (Jul 09, 2021)
8-37797446-G-A		not specified	Uncertain significance (Oct 06, 2021)
8-37797512-C-A		not specified	Uncertain significance (Apr 20, 2023)
8-37814918-A-G		not specified	Uncertain significance (Feb 28, 2023)
8-37814933-G-A		not specified	Uncertain significance (May 25, 2022)
8-37828896-G-C		not specified	Uncertain significance (Jun 17, 2022)
8-37829277-C-T		not specified	Uncertain significance (Feb 23, 2023)
8-37829298-G-A		not specified	Uncertain significance (Oct 06, 2022)
8-37829319-A-G		not specified	Uncertain significance (Nov 08, 2022)
8-37829329-G-A		not specified	Uncertain significance (Jul 20, 2022)
8-37829874-C-T		not specified	Uncertain significance (Sep 16, 2021)
8-37829952-C-T		not specified	Uncertain significance (Oct 06, 2021)
8-37829998-G-T		not specified	Uncertain significance (Jul 14, 2021)
8-37830746-C-A		not specified	Uncertain significance (Sep 17, 2021)
8-37830775-G-A		not specified	Uncertain significance (Dec 12, 2023)
8-37830832-T-C		not specified	Uncertain significance (Oct 03, 2022)
8-37830834-G-T		not specified	Uncertain significance (Feb 09, 2023)
8-37830869-A-G		not specified	Uncertain significance (Jul 05, 2023)
8-37830872-C-G		not specified	Uncertain significance (Jan 29, 2024)
8-37831448-G-T		not specified	Uncertain significance (Oct 29, 2021)
8-37831499-G-A		not specified	Uncertain significance (Jun 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ADGRA2	protein_coding	protein_coding	ENST00000412232	19	60706

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.50e-8	1.00	125692	0	55	125747	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.93	612	762	0.803	0.0000485	8376
Missense in Polyphen		193	263.78	0.73167		2973
Synonymous	0.0868	340	342	0.994	0.0000234	2909
Loss of Function	3.75	21	49.5	0.425	0.00000258	535

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000565	0.000548
Ashkenazi Jewish	0.00	0.00
East Asian	0.000171	0.000163
Finnish	0.000339	0.000323
European (Non-Finnish)	0.000247	0.000237
Middle Eastern	0.000171	0.000163
South Asian	0.0000655	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Endothelial receptor which functions as a WNT7-specific coactivator of canonical Wnt signaling (By similarity). Required for normal endothelial cell sprouting and migration in the forebrain and neural tube (By similarity). Has a major role in establishing the blood-brain barrier (By similarity). Binds to the glycosaminoglycans heparin, heparin sulfate, chondroitin sulfate and dermatan sulfate (PubMed:16982628). {ECO:0000250|UniProtKB:Q91ZV8, ECO:0000269|PubMed:22013897}.
• Pathway: Integrins in angiogenesis (Consensus)

Recessive Scores

• pRec: 0.124

Intolerance Scores

• rvis_EVS: -0.14
• rvis_percentile_EVS: 42.35

Haploinsufficiency Scores

• pHI: 0.310
• hipred: Y
• hipred_score: 0.660
• ghis: 0.527

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Adgra2
• Phenotype: craniofacial phenotype; growth/size/body region phenotype; normal phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); embryo phenotype; respiratory system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: adgra2
• Affected structure: melanocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: sprouting angiogenesis;G protein-coupled receptor signaling pathway;central nervous system development;positive regulation of endothelial cell migration;Wnt signaling pathway;endothelial cell migration;regulation of angiogenesis;regulation of chemotaxis;regulation of establishment of blood-brain barrier;positive regulation of canonical Wnt signaling pathway;negative regulation of vascular endothelial growth factor signaling pathway
• Cellular component: plasma membrane;cell surface;integral component of membrane;filopodium;Wnt signalosome
• Molecular function: G protein-coupled receptor activity;protein binding