ADGRG1
protein-codingadhesion G protein-coupled receptor G1, the group of Adhesion G protein-coupled receptors, subfamily G
Gene summary
This gene encodes a member of the G protein-coupled receptor family and regulates brain cortical patterning. The encoded protein binds specifically to transglutaminase 2, a component of tissue and tumor stroma implicated as an inhibitor of tumor progression. Mutations in this gene are associated with a brain malformation known as bilateral frontoparietal polymicrogyria. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]
- GPR56
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~54.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0011738
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0017091
Submitter: Natera
Inheritance Pattern: AR
Disease ID:MONDO:0011738
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0011738
Submitter: ClinGen
Bilateral Frontoparietal Polymicrogyria with linkage to chromosome 16 was initially described in 2003 by Chang et al. (PMID: 12730993) in 19 affected members from ten consanguineous families. Bilateral frontoparietal polymicrogyria (BFPP) manifests as increased gyral frequency with anterior predominance, cerebral white matter signal abnormalities, and cerebellar signal abnormalities on brain MRI; though originally described as polymicrogyria, subsequent histopathology has demonstrated that the increased gyral frequency actually represents a cobblestone malformation (PMID: 20929962). The disorder presents with hypotonia, developmental delay, moderate to severe intellectual disability, pyramidal signs, epileptic seizures, non progressive cerebellar ataxia, dysconjugate gaze and/or strabismus. First genotype-phenotype association was obtained in 2004 by Piao et al. (PMID:15044805) when all affected probands from PMID: 12730993 were found to carry homozygous variants of the ADGRG1 gene. ADGRG1 is a G protein-coupled receptor involved in cell-cell and cell-extracellular matrix interactions with a key role in cortical development. Structurally, it contains an ectodomain (ECD) with multiple protein motifs implicated in protein-protein interaction and glycosylation sites that mediate the adhesion function; a seven-pass transmembrane domain (7TM) responsible for signaling and a proteolysis site (GPS) crucial for the self-catalytic reaction. This reaction takes place in the ER and splits the receptor into an adhesion and a signaling (in the cell surface) subunit. The mechanism of pathogenicity is biallelic inherited loss-of-function (PMID: 21349848) variants. Seventeen missense, nine nonsense, six frameshift, one non frameshift and two splice site variants were reported in sixty-eight patients and two affected fetuses from forty-one families across twelve publications (PMIDs: 15044805, 16240336, 25642806, 35186395, 19016831, 20929962, 21723461, 23981349, 23274687, 29707406, 30982090, 36524291). Not all variants from the aforementioned PMIDs were scored because maximum genetic evidence points were reached. Additionally, a single report (PMID: 24531968) for autosomal recessive bilateral perisylvian polymicrogyria (associated with a 15-bp homozygous deletion located upstream of the transcriptional site of noncoding exon 1 of ADGRG1 gene) in three consanguineous families was not included for the purposes of this curation. The gene-disease relationship is supported by experimental evidence demonstrating preferential expression gene expression in neuronal progenitor cells of the cerebral cortical ventricular and subventricular zones during periods of neurogenesis but no expression in the cortical plate or intermediate zone (PMID: 15044805); the altered function in engineered cells with candidate pathogenic missense variants (PMID: 21349848); and neuropathological findings of an affected fetus terminated at 35 weeks of pregnancy which showed cobblestone-like and polymicrogyric cortex (PMID: 20929962). In summary, ADGRG1 is definitively associated with autosomal recessive Bilateral frontoparietal polymicrogyria. This has been repeatedly demonstrated and has been upheld over time. This was approved by the ClinGen Brain Malformation GCEP on October 24th, 2023.
Inheritance Pattern: AR
Disease ID:MONDO:0011738
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0011738
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Neurologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
Comments: Variants involving cis-regulatory elements have additionally been described
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ADGRG1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_201525.4. 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 | 7 | 348 | 2 | 357 | ||
| missense | 3 | 16 | 230 | 36 | 285 | |
| nonsense | 24 | 18 | 2 | 44 | ||
| start loss | 0 | |||||
| frameshift | 28 | 20 | 2 | 50 | ||
| splice donor/acceptor (+/-2bp) | 3 | 17 | 7 | 27 | ||
| Total | 58 | 71 | 248 | 384 | 2 | 763 |
Highest pathogenic variant AF is 0.00006190907
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_958933.1 | 13 | MANE Select | |
| Ensembl | ENSP00000455351.2 | 13 | MANE Select | |
| RefSeq | NP_001139242.1 | 13 | Standard | |
| RefSeq | NP_001139243.1 | 13 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| adgrg1 | Danio rerio | Structure: spinal cord Quality: has fewer parts of type abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- GPCRs, Other
Biological Process
- angiogenesis
- cell adhesion
- cell surface receptor signaling pathway
- G protein-coupled receptor signaling pathway
- adenylate cyclase-activating G protein-coupled receptor signaling pathway
Molecular Function
- G protein-coupled receptor activity
- collagen binding
- heparin binding
- extracellular matrix binding
Cellular Component
- integral component of plasma membrane
- integral component of membrane
- membrane raft
- extracellular exosome
- glial limiting end-foot
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000388812
- Coding exons
- 13
- Length
- 54381
- Individuals with no LoFs
- 125681
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 67
- Defined
- 125748
- p
- 0.000266
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0686 | 390 | 386 | 1.01 | 0.0000242 | 4508 |
| Missense (PolyPhen) | 106 | 122.54 | 0.865 | 1585 | ||
| Synonymous | -1.15 | 195 | 176 | 1.11 | 0.0000118 | 1450 |
| Loss of Function | 2.07 | 20 | 32.8 | 0.610 | 0.00000189 | 330 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.00029 | 0.00029 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00027 | 0.00027 | rare |
| Finnish | 0.000047 | 0.000046 | rare |
| European (Non-Finnish) | 0.00022 | 0.00022 | rare |
| South Asian | 0.00069 | 0.00069 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Receptor involved in cell adhesion and probably in cell- cell interactions. Mediates cell matrix adhesion in developing neurons and hematopoietic stem cells. Receptor for collagen III/COL3A1 in the developing brain and involved in regulation of cortical development, specifically in maintenance of the pial basement membrane integrity and in cortical lamination (By similarity). Binding to the COL3A1 ligand inhibits neuronal migration and activates the RhoA pathway by coupling to GNA13 and possibly GNA12 (PubMed:22238662). Plays a role in the maintenance of hematopoietic stem cells and/or leukemia stem cells in bone marrow niche (By similarity). Plays a critical role in cancer progression by inhibiting VEGFA production threreby inhibiting angiogenesis through a signaling pathway mediated by PRKCA (PubMed:16757564, PubMed:21724588). Plays an essential role in testis development (By similarity). {ECO:0000250|UniProtKB:Q8K209, ECO:0000269|PubMed:16757564, ECO:0000269|PubMed:19572147, ECO:0000269|PubMed:21708946, ECO:0000269|PubMed:21724588, ECO:0000269|PubMed:22238662, ECO:0000269|PubMed:24531968}.;
- Disease
- DISEASE: Polymicrogyria, bilateral frontoparietal (BFPP) [MIM:606854]: A malformation of the cortex in which the brain surface is irregular and characterized by an excessive number of small gyri with abnormal lamination, most severe in the frontoparietal regions. BFPP clinical manifestations include developmental and psychomotor delay, cerebellar and pyramidal signs, truncal ataxia, seizures, hyperreflexia. Polymicrogyria is a heterogeneous disorder, considered to be the result of postmigratory abnormal cortical organization. {ECO:0000269|PubMed:15044805, ECO:0000269|PubMed:16240336, ECO:0000269|PubMed:21349848, ECO:0000269|PubMed:21723461, ECO:0000269|PubMed:22238662, ECO:0000269|PubMed:24949629}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Polymicrogyria, bilateral perisylvian, autosomal recessive (BPPR) [MIM:615752]: A form of polymicrogyria, a malformation of the cortex in which the brain surface is irregular and characterized by an excessive number of small gyri with abnormal lamination. BPPR is characterized by strikingly restricted polymicrogyria limited to the cortex surrounding the Sylvian fissure. Affected individuals have intellectual and language difficulty and seizures, but no motor disability. Polymicrogyria is a heterogeneous disorder, considered to be the result of post-migratory abnormal cortical organization. {ECO:0000269|PubMed:24531968}. Note=The disease is caused by mutations affecting the gene represented in this entry. Homozygous deletion of 1 of 2 tandem 15-bp repeats located 144 bp upstream of the ADGRG1 non-coding exon 1m transcription start site, results in impaired perisylvian ADGRG1 expression and disruption of perisylvian gyri (PubMed:24531968). {ECO:0000269|PubMed:24531968}.;
Recessive Scores
- pRec
- 0.142
Intolerance Scores
- RVIS EVS
- -0.51
- RVIS percentile EVS
- 21.77
Essentials
- Essential (gene trap)
- N