ADGRA3

protein-coding

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

Gene summary

This gene encodes a member of the G protein-coupled receptor superfamily. This membrane protein may play a role in tumor angiogenesis through its interaction with the human homolog of the Drosophila disc large tumor suppressor gene. This gene is mapped to a candidate region of chromosome 4 which may be associated with bipolar disorder and schizophrenia. [provided by RefSeq, Oct 2012]

Previous symbols:

GPR125

MANE transcript

NM_145290.4

Inheritance

ClinVar variants

U:701B:270

Top phenotype

Retinal dystrophy

gnomAD constraint

pLI —, LoF o/e 0.23

Max pathogenic AF

—

Genomic locus

chr4:22,345,071-22,516,066

External References & Databases

Ensembl (ENSG00000152990)

Transcript & Mutation Effects

hg38 • Region Span ~171.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

retinitis pigmentosaLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0019200

Submitter: PanelApp Australia

retinitis pigmentosaLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0019200

Submitter: G2P

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ADGRA3 variants in ClinVar

7 Conditions Cataloged

not providedTotal: 1003

not specifiedTotal: 233

Retinal dystrophyTotal: 73

ADGRA3-related disorderTotal: 32

Optic atrophyTotal: 2

Retinitis pigmentosaTotal: 1

Autosomal recessive retinitis pigmentosaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_145290.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			11 clinvar	228 clinvar	11 clinvar	250
missense			655 clinvar	22 clinvar	9 clinvar	686
nonsense			11 clinvar			11
start loss			1 clinvar			1
frameshift			16 clinvar			16
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	701	250	20	971

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_145290.4	RefSeq	NP_660333.2	19	MANE Select
ENST00000334304.10	Ensembl	ENSP00000334952.5	19	MANE Select
ENST00000502482.1	Ensembl	ENSP00000421006.1	12	Standard
ENST00000502482.2	Ensembl	ENSP00000421006.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell surface receptor signaling pathway
G protein-coupled receptor signaling pathway

Molecular Function

G protein-coupled receptor activity

Cellular Component

external side of plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000334304
Coding exons: 19
Length: 170984
Individuals with no LoFs: 125699
Homozygous LoFs: 0
Heterozygous LoFs: 49
Defined: 125748
p: 0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.451	694	728	0.953	0.0000407	8572
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.00023	0.00023	rare
European (Non-Finnish)	0.00016	0.00016	rare
South Asian	0.00056	0.00056	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (gene trap): N