ADGRA3

adhesion G protein-coupled receptor A3, the group of Adhesion G protein-coupled receptors, subfamily A|I-set domain containing

Basic information

Region (hg38): 4:22345071-22516066

Previous symbols: [ "GPR125" ]

Links

ENSG00000152990 ∙ NCBI:166647 ∙ OMIM:612303 ∙ HGNC:13839 ∙ Uniprot:Q8IWK6 ∙ 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 ADGRA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADGRA3 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			11	191	13	215
missense			518	14	10	542
nonsense			9			9
start loss			1			1
frameshift			13			13
inframe indel			15	1		16
splice donor/acceptor (+/-2bp)			5			5
splice region			17	22		39
non coding			3	65	7	75
Total	0	0	575	271	30

Variants in ADGRA3

This is a list of pathogenic ClinVar variants found in the ADGRA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-22387712-G-A			Uncertain significance (Nov 27, 2023)
4-22387712-GT-G			Uncertain significance (Aug 16, 2023)
4-22387720-G-A			Likely benign (Jun 25, 2023)
4-22387720-G-C			Uncertain significance (Oct 19, 2022)
4-22387739-C-T			Uncertain significance (Jul 20, 2022)
4-22387745-T-C			Uncertain significance (Sep 25, 2022)
4-22387748-C-A			Uncertain significance (Dec 30, 2022)
4-22387752-T-G			Uncertain significance (Oct 02, 2023)
4-22387755-T-A		not specified	Uncertain significance (Dec 28, 2022)
4-22387758-C-T			Uncertain significance (Jul 29, 2022)
4-22387759-G-A		ADGRA3-related disorder	Likely benign (Jan 15, 2024)
4-22387764-C-A		not specified • Retinal dystrophy	Uncertain significance (Jan 22, 2024)
4-22387764-C-T		Retinal dystrophy	Uncertain significance (Oct 01, 2023)
4-22387778-T-G		Retinal dystrophy	Uncertain significance (Oct 01, 2023)
4-22387786-A-T			Uncertain significance (Dec 20, 2019)
4-22387794-T-C			Uncertain significance (Aug 07, 2022)
4-22387796-A-G			Uncertain significance (Oct 11, 2021)
4-22387800-G-A			Uncertain significance (Aug 04, 2021)
4-22387805-T-C			Uncertain significance (Mar 19, 2022)
4-22387809-G-A			Uncertain significance (Jun 23, 2022)
4-22387819-G-A			Likely benign (Jun 27, 2022)
4-22387824-G-A			Uncertain significance (Jun 15, 2022)
4-22387826-C-G			Uncertain significance (Sep 22, 2021)
4-22387826-C-T			Uncertain significance (Oct 13, 2022)
4-22387828-A-G			Likely benign (Nov 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ADGRA3	protein_coding	protein_coding	ENST00000334304	19	170984

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.293	0.707	125699	0	49	125748	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.451	694	728	0.953	0.0000407	8572
Missense in Polyphen		231	267.02	0.86511		3124
Synonymous	-0.714	295	280	1.05	0.0000168	2641
Loss of Function	5.57	14	60.9	0.230	0.00000335	718

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000117	0.000117
Ashkenazi Jewish	0.00	0.00
East Asian	0.000223	0.000217
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000159	0.000158
Middle Eastern	0.000223	0.000217
South Asian	0.000555	0.000555
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Orphan receptor that may have a role in planar cell polarity pathway. {ECO:0000250|UniProtKB:S4X0Q8}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• rvis_EVS: -0.07
• rvis_percentile_EVS: 47.8

Haploinsufficiency Scores

• pHI: 0.0825
• hipred: N
• hipred_score: 0.466
• ghis: 0.504

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Adgra3
• Phenotype: normal phenotype

Gene ontology

• Biological process: cell surface receptor signaling pathway;G protein-coupled receptor signaling pathway
• Cellular component: external side of plasma membrane;integral component of membrane
• Molecular function: G protein-coupled receptor activity