GeneBe

GPRC5B

G protein-coupled receptor class C group 5 member B, the group of G protein-coupled receptors, Class C orphans

Basic information

Region (hg38): 16:19856691-19886167

Links

ENSG00000167191 ∙ NCBI:51704 ∙ OMIM:605948 ∙ HGNC:13308 ∙ Uniprot:Q9NZH0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • megalencephalic leukoencephalopathy with subcortical cysts 1 (Strong), mode of inheritance: AD
  • megalencephalic leukoencephalopathy with subcortical cysts 3 (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Megalencephalic leukoencephalopathy with subcortical cysts 3ADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingNeurologic37143309

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GPRC5B gene.

  • not_specified (49 variants)
  • not_provided (4 variants)
  • Megalencephalic_leukoencephalopathy_with_subcortical_cysts_3 (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPRC5B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016235.3. 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
2
clinvar
 3
missense
49
clinvar
1
clinvar
1
clinvar
 51
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 49 2 3
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
GPRC5Bprotein_codingprotein_codingENST00000300571 328874
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.02420.9631257310171257480.0000676
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.322002600.7690.00001702602
Missense in Polyphen86122.960.69941236
Synonymous-0.7171311211.080.00000926876
Loss of Function2.19513.70.3648.08e-7121

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002060.000206
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.00007090.0000703
Middle Eastern0.00005440.0000544
South Asian0.00006530.0000653
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Unknown. This retinoic acid-inducible G-protein coupled receptor provide evidence for a possible interaction between retinoid and G-protein signaling pathways.;
Pathway
GPCRs, Class C Metabotropic glutamate, pheromone (Consensus)

Recessive Scores

pRec
0.135

Intolerance Scores

loftool
0.107
rvis_EVS
-0.82
rvis_percentile_EVS
11.88

Haploinsufficiency Scores

pHI
0.728
hipred
Y
hipred_score
0.768
ghis
0.654

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.460

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Gprc5b
Phenotype
homeostasis/metabolism phenotype; 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); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Gene ontology

Biological process
G protein-coupled receptor signaling pathway;locomotory behavior;positive regulation of neuron projection development;activation of protein kinase activity;glucose homeostasis;positive regulation of I-kappaB kinase/NF-kappaB signaling;positive regulation of neuron differentiation;positive regulation of inflammatory response;positive regulation of macrophage cytokine production;positive regulation of protein tyrosine kinase activity;positive regulation of canonical Wnt signaling pathway
Cellular component
extracellular space;nucleus;nucleolus;cytosol;plasma membrane;cell surface;integral component of membrane;cytoplasmic vesicle membrane;intracellular membrane-bounded organelle;receptor complex;extracellular exosome
Molecular function
G protein-coupled receptor binding;G protein-coupled receptor activity;protein kinase binding;protein kinase activator activity