GFRA3 (GDNF family receptor alpha 3) - Rat Genome Database

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Gene: GFRA3 (GDNF family receptor alpha 3) Homo sapiens
Analyze
Symbol: GFRA3
Name: GDNF family receptor alpha 3
RGD ID: 731370
HGNC Page HGNC
Description: Predicted to enable glial cell-derived neurotrophic factor receptor activity. Predicted to be involved in nervous system development. Predicted to act upstream of or within axon guidance; neuron migration; and sympathetic nervous system development. Located in cytosol and plasma membrane.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: GDNF family receptor alpha-3; GDNF receptor alpha-3; gdnf-family receptor alpha 3; GDNFR-alpha-3; GDNFR3; GFR-alpha-3; glial cell line-derived neurotrophic factor receptor alpha-3; GPI-linked receptor
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl5138,252,380 - 138,274,621 (-)EnsemblGRCh38hg38GRCh38
GRCh385138,252,380 - 138,274,621 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh375137,588,069 - 137,610,310 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 365137,615,968 - 137,638,152 (-)NCBINCBI36hg18NCBI36
Build 345137,615,969 - 137,638,152NCBI
Celera5133,709,300 - 133,731,054 (-)NCBI
Cytogenetic Map5q31.2NCBI
HuRef5132,779,039 - 132,801,225 (-)NCBIHuRef
CHM1_15137,020,644 - 137,042,862 (-)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

Additional References at PubMed
PMID:7829101   PMID:9407096   PMID:9490034   PMID:9576965   PMID:9883723   PMID:10978357   PMID:11360200   PMID:12477932   PMID:12490080   PMID:12624147   PMID:12975309   PMID:15340161  
PMID:15489334   PMID:16765900   PMID:16773224   PMID:18029348   PMID:19304517   PMID:20116071   PMID:21873635   PMID:22031517   PMID:22610502   PMID:23351331   PMID:24952745   PMID:25056061  
PMID:26984265   PMID:28356515   PMID:28651425   PMID:29987050   PMID:31615875  


Genomics

Comparative Map Data
GFRA3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl5138,252,380 - 138,274,621 (-)EnsemblGRCh38hg38GRCh38
GRCh385138,252,380 - 138,274,621 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh375137,588,069 - 137,610,310 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 365137,615,968 - 137,638,152 (-)NCBINCBI36hg18NCBI36
Build 345137,615,969 - 137,638,152NCBI
Celera5133,709,300 - 133,731,054 (-)NCBI
Cytogenetic Map5q31.2NCBI
HuRef5132,779,039 - 132,801,225 (-)NCBIHuRef
CHM1_15137,020,644 - 137,042,862 (-)NCBICHM1_1
Gfra3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391834,822,951 - 34,853,440 (-)NCBIGRCm39mm39
GRCm39 Ensembl1834,822,951 - 34,853,440 (-)Ensembl
GRCm381834,689,898 - 34,720,387 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1834,689,898 - 34,720,387 (-)EnsemblGRCm38mm10GRCm38
MGSCv371834,849,557 - 34,880,041 (-)NCBIGRCm37mm9NCBIm37
MGSCv361834,814,720 - 34,845,131 (-)NCBImm8
Celera1835,142,994 - 35,173,839 (-)NCBICelera
Cytogenetic Map18B1NCBI
Gfra3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21826,297,828 - 26,326,105 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1826,297,829 - 26,326,105 (-)Ensembl
Rnor_6.01827,491,860 - 27,520,133 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1827,491,845 - 27,520,295 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01827,205,217 - 27,233,490 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41827,167,576 - 27,195,848 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11827,195,323 - 27,208,736 (-)NCBI
Celera1826,035,434 - 26,063,700 (-)NCBICelera
Cytogenetic Map18p12NCBI
Gfra3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554182,143,169 - 2,163,286 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554182,152,887 - 2,162,883 (+)NCBIChiLan1.0ChiLan1.0
GFRA3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15139,762,690 - 139,784,942 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5139,762,690 - 139,784,942 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v05133,630,274 - 133,652,525 (-)NCBIMhudiblu_PPA_v0panPan3
GFRA3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11125,881,523 - 25,897,863 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1125,882,099 - 25,897,817 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1124,652,055 - 24,667,781 (-)NCBI
ROS_Cfam_1.01126,738,265 - 26,754,257 (-)NCBI
UMICH_Zoey_3.11125,445,543 - 25,461,486 (-)NCBI
UNSW_CanFamBas_1.01125,268,312 - 25,284,034 (-)NCBI
UU_Cfam_GSD_1.01125,932,678 - 25,948,643 (-)NCBI
Gfra3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213154,146,854 - 154,167,704 (+)NCBI
SpeTri2.0NW_0049365317,443,842 - 7,457,518 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GFRA3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.12140,263,297 - 140,283,227 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22145,962,140 - 145,982,527 (-)NCBISscrofa10.2Sscrofa10.2susScr3
GFRA3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12340,927,283 - 40,948,591 (-)NCBI
ChlSab1.1 Ensembl2340,927,289 - 40,946,023 (-)Ensembl
Vero_WHO_p1.0NW_02366603436,940,183 - 36,964,179 (+)NCBI
Gfra3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474331,079,591 - 31,095,595 (-)NCBI

Position Markers
RH99221  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh375137,588,085 - 137,588,268UniSTSGRCh37
Build 365137,615,984 - 137,616,167RGDNCBI36
Celera5133,709,316 - 133,709,499RGD
Cytogenetic Map5q31.1-q31.3UniSTS
GeneMap99-GB4 RH Map5524.46UniSTS
GFRA3_3327  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh375137,587,939 - 137,588,708UniSTSGRCh37
Build 365137,615,838 - 137,616,607RGDNCBI36
Celera5133,709,170 - 133,709,939RGD
HuRef5132,778,909 - 132,779,678UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:802
Count of miRNA genes:343
Interacting mature miRNAs:354
Transcripts:ENST00000274721, ENST00000378362
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High 1
Medium 964 127 42 21 29 17 797 550 812 14 302 35 4 56 660
Low 1310 1624 1043 208 274 60 2397 741 791 131 996 920 150 1 868 1225 1
Below cutoff 121 922 513 297 1041 290 1029 817 1773 160 132 574 18 263 822 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000274721   ⟹   ENSP00000274721
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl5138,252,380 - 138,274,621 (-)Ensembl
RefSeq Acc Id: ENST00000378362   ⟹   ENSP00000367613
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl5138,252,382 - 138,274,565 (-)Ensembl
RefSeq Acc Id: NM_001496   ⟹   NP_001487
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385138,252,380 - 138,274,621 (-)NCBI
GRCh375137,588,069 - 137,610,544 (-)NCBI
Build 365137,615,968 - 137,638,152 (-)NCBI Archive
HuRef5132,779,039 - 132,801,225 (-)ENTREZGENE
CHM1_15137,020,644 - 137,042,862 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001487   ⟸   NM_001496
- Peptide Label: preproprotein
- UniProtKB: O60609 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000367613   ⟸   ENST00000378362
RefSeq Acc Id: ENSP00000274721   ⟸   ENST00000274721

Promoters
RGD ID:6870698
Promoter ID:EPDNEW_H8514
Type:initiation region
Name:GFRA3_1
Description:GDNF family receptor alpha 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh385138,274,478 - 138,274,538EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 5q23.3-33.2(chr5:130860928-155321811)x3 copy number gain See cases [RCV000051193] Chr5:130860928..155321811 [GRCh38]
Chr5:130196621..154701371 [GRCh37]
Chr5:130224520..154681564 [NCBI36]
Chr5:5q23.3-33.2
pathogenic
GRCh38/hg38 5q31.1-31.2(chr5:133401565-138437038)x1 copy number loss See cases [RCV000052114] Chr5:133401565..138437038 [GRCh38]
Chr5:132737257..137772727 [GRCh37]
Chr5:132765156..137800626 [NCBI36]
Chr5:5q31.1-31.2
pathogenic
GRCh38/hg38 5q21.3-33.2(chr5:106619588-156124387)x1 copy number loss See cases [RCV000053524] Chr5:106619588..156124387 [GRCh38]
Chr5:105955289..155551397 [GRCh37]
Chr5:105983188..155483975 [NCBI36]
Chr5:5q21.3-33.2
pathogenic
NM_001496.4(GFRA3):c.1135C>A (p.Pro379Thr) single nucleotide variant Malignant tumor of prostate [RCV000149116] Chr5:138253036 [GRCh38]
Chr5:137588725 [GRCh37]
Chr5:5q31.2
uncertain significance
GRCh38/hg38 5q31.1-31.3(chr5:135297294-140106003)x3 copy number gain See cases [RCV000133750] Chr5:135297294..140106003 [GRCh38]
Chr5:134632984..139485588 [GRCh37]
Chr5:134660883..139465772 [NCBI36]
Chr5:5q31.1-31.3
pathogenic
GRCh38/hg38 5q31.2-31.3(chr5:137836682-140696361)x3 copy number gain See cases [RCV000134725] Chr5:137836682..140696361 [GRCh38]
Chr5:137172371..140075946 [GRCh37]
Chr5:137200270..140056130 [NCBI36]
Chr5:5q31.2-31.3
pathogenic
GRCh38/hg38 5q31.2(chr5:138179894-139039890)x3 copy number gain See cases [RCV000135679] Chr5:138179894..139039890 [GRCh38]
Chr5:137515583..138375579 [GRCh37]
Chr5:137543482..138403478 [NCBI36]
Chr5:5q31.2
uncertain significance
GRCh38/hg38 5q23.3-33.2(chr5:129847794-153353546)x3 copy number gain See cases [RCV000138808] Chr5:129847794..153353546 [GRCh38]
Chr5:129183487..152733106 [GRCh37]
Chr5:129211386..152713299 [NCBI36]
Chr5:5q23.3-33.2
pathogenic
GRCh37/hg19 5q15-35.3(chr5:94844077-178830410)x3 copy number gain not provided [RCV000487658] Chr5:94844077..178830410 [GRCh37]
Chr5:5q15-35.3
likely benign
GRCh37/hg19 5q23.3-33.3(chr5:130125085-157574910)x3 copy number gain See cases [RCV000449349] Chr5:130125085..157574910 [GRCh37]
Chr5:5q23.3-33.3
pathogenic
GRCh37/hg19 5p15.33-q35.3(chr5:113577-180719789) copy number gain See cases [RCV000510723] Chr5:113577..180719789 [GRCh37]
Chr5:5p15.33-q35.3
pathogenic
GRCh37/hg19 5q21.3-35.3(chr5:106716357-180687338)x3 copy number gain See cases [RCV000448245] Chr5:106716357..180687338 [GRCh37]
Chr5:5q21.3-35.3
pathogenic
NC_000005.9:g.(?_86400000)_(154000000_?)del deletion Familial adenomatous polyposis 1 [RCV001381154]|Hereditary cancer-predisposing syndrome [RCV000554476] Chr5:86400000..154000000 [GRCh37]
Chr5:5q14.3-33.2
pathogenic
GRCh37/hg19 5p15.1-q35.2(chr5:17628741-176575720)x1 copy number loss See cases [RCV000511978] Chr5:17628741..176575720 [GRCh37]
Chr5:5p15.1-q35.2
pathogenic
GRCh37/hg19 5p15.33-q35.3(chr5:113577-180719789)x3 copy number gain See cases [RCV000512039] Chr5:113577..180719789 [GRCh37]
Chr5:5p15.33-q35.3
pathogenic
GRCh37/hg19 5p15.33-q35.3(chr5:13648-180905029)x3 copy number gain not provided [RCV000744317] Chr5:13648..180905029 [GRCh37]
Chr5:5p15.33-q35.3
pathogenic
GRCh37/hg19 5p15.33-q35.3(chr5:25328-180693344)x3 copy number gain not provided [RCV000744323] Chr5:25328..180693344 [GRCh37]
Chr5:5p15.33-q35.3
pathogenic
Single allele deletion Neurodevelopmental disorder [RCV000787436] Chr5:14685137..149511942 [GRCh37]
Chr5:5p15.2-q32
uncertain significance
NM_001496.4(GFRA3):c.948C>T (p.Cys316=) single nucleotide variant not provided [RCV000956310] Chr5:138253842 [GRCh38]
Chr5:137589531 [GRCh37]
Chr5:5q31.2
benign
NC_000005.9:g.(?_136633338)_(140998481_?)dup duplication Deafness, autosomal dominant 1 [RCV001319817]|Mental retardation, autosomal dominant 31 [RCV001339088] Chr5:136633338..140998481 [GRCh37]
Chr5:5q31.2-31.3
uncertain significance
GRCh37/hg19 5q31.2(chr5:136409875-137739167) copy number loss Microcephaly [RCV001352638] Chr5:136409875..137739167 [GRCh37]
Chr5:5q31.2
pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:4245 AgrOrtholog
COSMIC GFRA3 COSMIC
Ensembl Genes ENSG00000146013 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSP00000274721 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000367613 UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000274721 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000378362 UniProtKB/Swiss-Prot
GTEx ENSG00000146013 GTEx
HGNC ID HGNC:4245 ENTREZGENE
Human Proteome Map GFRA3 Human Proteome Map
InterPro GDNF/GAS1 UniProtKB/Swiss-Prot
  GDNF_alpha UniProtKB/Swiss-Prot
  GDNF_rcpt UniProtKB/Swiss-Prot
  GDNF_rcpt_A3 UniProtKB/Swiss-Prot
KEGG Report hsa:2676 UniProtKB/Swiss-Prot
NCBI Gene 2676 ENTREZGENE
OMIM 605710 OMIM
PANTHER PTHR10269 UniProtKB/Swiss-Prot
Pfam GDNF UniProtKB/Swiss-Prot
PharmGKB PA28655 PharmGKB
PRINTS GDNFRALPHA3 UniProtKB/Swiss-Prot
  GDNFRECEPTOR UniProtKB/Swiss-Prot
SMART GDNF UniProtKB/Swiss-Prot
Superfamily-SCOP SSF110035 UniProtKB/Swiss-Prot
UniProt GFRA3_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary B2RA36 UniProtKB/Swiss-Prot
  B4DMY9 UniProtKB/Swiss-Prot
  Q6UW20 UniProtKB/Swiss-Prot
  Q8IUZ2 UniProtKB/Swiss-Prot