GFRA3

GDNF family receptor alpha 3

Basic information

Region (hg38): 5:138252379-138274621

Links

ENSG00000146013 ∙ NCBI:2676 ∙ OMIM:605710 ∙ HGNC:4245 ∙ Uniprot:O60609 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GFRA3 gene.

• Inborn genetic diseases (10 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GFRA3 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	1

Variants in GFRA3

This is a list of pathogenic ClinVar variants found in the GFRA3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-138253036-G-T		Malignant tumor of prostate	Uncertain significance (-)
5-138253842-G-A			Benign (Jul 31, 2018)
5-138253846-C-G		not specified	Uncertain significance (Oct 12, 2021)
5-138257648-G-A		not specified	Uncertain significance (Aug 02, 2022)
5-138257711-T-C		not specified	Likely benign (Aug 15, 2023)
5-138257729-C-T		not specified	Uncertain significance (Jun 28, 2022)
5-138257799-C-G		not specified	Uncertain significance (Dec 28, 2022)
5-138257919-A-G		not specified	Uncertain significance (Dec 14, 2023)
5-138259614-T-C		not specified	Uncertain significance (Apr 18, 2023)
5-138259629-A-G		not specified	Uncertain significance (Jan 24, 2024)
5-138264269-C-T		not specified	Uncertain significance (Jan 19, 2022)
5-138264326-C-T		not specified	Uncertain significance (Jun 11, 2021)
5-138264334-C-T		not specified	Uncertain significance (Dec 05, 2022)
5-138274391-G-T		not specified	Uncertain significance (Sep 29, 2022)
5-138274421-C-T		not specified	Uncertain significance (Aug 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GFRA3	protein_coding	protein_coding	ENST00000274721	8	22293

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0276	0.970	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.05	153	243	0.630	0.0000146	2587
Missense in Polyphen		44	92.368	0.47635		1011
Synonymous	0.837	87	97.5	0.892	0.00000582	812
Loss of Function	2.69	6	18.5	0.324	0.00000105	190

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000921	0.0000919
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000537	0.0000462
European (Non-Finnish)	0.0000534	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for the glial cell line-derived neurotrophic factor, ARTN (artemin). Mediates the artemin-induced autophosphorylation and activation of the RET receptor tyrosine kinase. {ECO:0000269|PubMed:9883723}.
• Pathway: Developmental Biology;Signal Transduction;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;RET signaling;Axon guidance (Consensus)

Recessive Scores

• pRec: 0.139

Intolerance Scores

• loftool: 0.472
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.37

Haploinsufficiency Scores

• pHI: 0.461
• hipred: Y
• hipred_score: 0.571
• ghis: 0.533

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.802

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Gfra3
• Phenotype: 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); cellular phenotype

Zebrafish Information Network

• Gene name: gfra3
• Affected structure: adductor hyohyoid
• Phenotype tag: abnormal
• Phenotype quality: lacks parts or has fewer parts of type

Gene ontology

• Biological process: MAPK cascade;neuron migration;signal transduction;nervous system development;axon guidance;peripheral nervous system development;sympathetic nervous system development
• Cellular component: cytosol;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;signaling receptor binding;protein binding;axon guidance receptor activity