GFRA2

GDNF family receptor alpha 2

Basic information

Region (hg38): 8:21690398-21812357

Links

ENSG00000168546NCBI:2675OMIM:601956HGNC:4244Uniprot:O00451AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GFRA2 gene.

  • not_specified (57 variants)
  • not_provided (2 variants)
  • Pazopanib_response (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GFRA2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001495.5. 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
1
missense
57
clinvar
1
clinvar
1
clinvar
59
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 57 1 2
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
GFRA2protein_codingprotein_codingENST00000524240 9121955
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.09750.896124646061246520.0000241
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.1411911970.9720.00001293011
Missense in Polyphen4968.7370.712871014
Synonymous-1.4410083.31.200.00000568914
Loss of Function2.36413.30.3027.27e-7237

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00005920.0000592
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00002820.0000265
Middle Eastern0.000.00
South Asian0.00003430.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Receptor for neurturin. Mediates the NRTN-induced autophosphorylation and activation of the RET receptor. Also able to mediate GDNF signaling through the RET tyrosine kinase receptor.;
Pathway
Developmental Biology;Signal Transduction;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;NCAM signaling for neurite out-growth;NCAM1 interactions;RET signaling;Axon guidance (Consensus)

Recessive Scores

pRec
0.145

Haploinsufficiency Scores

pHI
0.318
hipred
N
hipred_score
0.361
ghis
0.551

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.865

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyHighMediumHigh
CancerHighMediumHigh

Mouse Genome Informatics

Gene name
Gfra2
Phenotype
behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process
MAPK cascade;transmembrane receptor protein tyrosine kinase signaling pathway;nervous system development;axon guidance;glial cell-derived neurotrophic factor receptor signaling pathway
Cellular component
plasma membrane;external side of plasma membrane;extrinsic component of membrane;anchored component of membrane;receptor complex
Molecular function
Ras guanyl-nucleotide exchange factor activity;glial cell-derived neurotrophic factor receptor activity