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

• retinitis pigmentosa (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ADGRA3 gene.

• not_provided (941 variants)
• not_specified (203 variants)
• Retinal_dystrophy (73 variants)
• ADGRA3-related_disorder (24 variants)
• Optic_atrophy (2 variants)
• Retinitis_pigmentosa (1 variants)
• Autosomal_recessive_retinitis_pigmentosa (1 variants)

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. These statistics are base on transcript: NM_000145290.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			12	213	11	236
missense			607	19	9	635
nonsense			11			11
start loss			1			1
frameshift			16			16
splice donor/acceptor (+/-2bp)			5			5
Total	0	0	652	232	20

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