Gfra1 Gene Detail

Summary

• Symbol
  Gfra1
• Name
  glial cell line derived neurotrophic factor family receptor alpha 1
• Synonyms
  GDNFR-alpha, GFR alpha-1

• Feature Type
  protein coding gene
• IDs
  MGI:1100842
  NCBI Gene: 14585
• Alliance
  gene page
• Transcription Start Sites
  19 TSS
• Candidate for QTL
  6 QTL

Location &
Maps

• Sequence Map
  Chr19:58224036-58444341 bp, - strand

  From Ensembl annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 19, 54.18 cM, cytoband D2-D3
• Mapping Data
  5 experiments

Strain
Comparison

• SNPs within 2kb
  12798 from dbSNP Build 142
• Strain Annotations
  18

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1100842	protein coding gene	Chr19:58224013-58444387 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0025276	protein coding gene	Chr19:58704600-58930825 (-)
A/J	MGP_AJ_G0025252	protein coding gene	Chr19:55809934-56032271 (-)
AKR/J	MGP_AKRJ_G0025221	protein coding gene	Chr19:57562567-57791063 (-)
BALB/cJ	MGP_BALBcJ_G0025247	protein coding gene	Chr19:55882809-56103584 (-)
C3H/HeJ	MGP_C3HHeJ_G0025007	protein coding gene	Chr19:57798140-58029523 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0025690	protein coding gene	Chr19:60107855-60345550 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0023102	protein coding gene	Chr19:54702087-54926391 (-)
CAST/EiJ	MGP_CASTEiJ_G0024472	protein coding gene	Chr19:57868101-58100349 (-)
CBA/J	MGP_CBAJ_G0024987	protein coding gene	Chr19:63046863-63287832 (-)
DBA/2J	MGP_DBA2J_G0025119	protein coding gene	Chr19:55565779-55786414 (-)
FVB/NJ	MGP_FVBNJ_G0025080	protein coding gene	Chr19:55297094-55521006 (-)
LP/J	MGP_LPJ_G0025205	protein coding gene	Chr19:58561712-58789379 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0025113	protein coding gene	Chr19:62293665-62546422 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0025748	protein coding gene	Chr19:57786071-58014996 (-)
PWK/PhJ	MGP_PWKPhJ_G0024220	protein coding gene	Chr19:55557553-55781068 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0024023	protein coding gene	Chr19:56458962-56688116 (-)
WSB/EiJ	MGP_WSBEiJ_G0024542	protein coding gene	Chr19:57900369-58132940 (-)

Homology

• Human Ortholog
  GFRA1, GDNF family receptor alpha 1

• Vertebrate Orthologs
  4

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  GFRA1, GDNF family receptor alpha 1
  
• Synonyms
  GDNFR, GDNFRA, GDNFR-alpha-1, GFRalpha-1, GFR-ALPHA-1, RET1L, RETL1, RHDA4, TRNR1
• Links
  HGNC:4243

  NCBI Gene ID: 2674

  UniProt: P56159

  
  
• Chr Location
  10q25.3; chr10:116056925-116276803 (-)  GRCh38

---

• MGI Vertebrate Homology
  Gfra1 stringent orthology
  1 human;1 mouse;1 rat;2 zebrafish
  
• HCOP
  vertebrate homology predictions: GFRA1
• Protein SuperFamily
  GDNF_family_receptor_alpha
• Gene Tree
  Gfra1
  

Human Diseases

• Diseases
  1 with Gfra1 mouse models; 1 with human GFRA1 associations

Human Disease

Mouse Models

Hirschsprung's disease

IDs

Hirschsprung's disease      

DOID:10487
ICD10CM:Q43.1
MESH:D006627
NCI:C34700
OMIM:600156
OMIM:606874
OMIM:606875
OMIM:608462
OMIM:611644
ORDO:388
UMLS_CUI:C0019569

View 2 models

Mouse Models

Human Disease Modeled: Hirschsprung's disease

Allelic Composition	Genetic Background	Reference	Phenotypes
Gfra1tm1Jmi/Gfra1tm1Jmi	involves: 129X1/SvJ * C57BL/6	J:49471	View
Gfra1tm1Jmi/Gfra1tm2Jmi Tg(CAG-cre/Esr1*)5Amc/0	involves: 129/Sv * C57BL/6 * CBA * SJL	J:122607	View

renal agenesis

IDs

renal agenesis      

DOID:14766
MESH:C563261
OMIM:191830
ORDO:93108

Click on a disease name to see all genes associated with that disease.

• Mutations/Alleles
  2 with disease annotations

• References
  2 with disease annotations

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  54 phenotypes from 7 alleles in 8 genetic backgrounds
  5 phenotypes from multigenic genotypes
  67 phenotype references
  

• All Mutations and Alleles
  23
• Endonuclease-mediated
  4
• Gene trapped
  4
• Targeted
  14
• Transgenic
  1
• Incidental Mutations
  Mutagenetix , APF
• Find Mice (IMSR)
  31 strains or lines available
• Comparison Matrix
  Gene Expression + Phenotype
• Recombinase Activity
  Comparison Matrix Gene Expression + Recombinase Activity

Homozygotes for targeted null mutations lack kidneys and enteric neurons resulting in neonatal lethality.

Gene Ontology
(GO)
Classifications

• All GO Annotations
  57
• GO References
  14

Expression

• Assay Results
  1359
• Tissues
  250
• cDNA Data
  75
• Literature Summary
  132

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas
• Other Vertebrate Links
  GEISHA GFRA1
  Xenbase gfra1
  ZFIN gfra1a, gfra1b

Sequences &
Gene Models

• All Sequences
  86
• RefSeq
  15
• UniProt
  11
• CCDS
  CCDS38028.1, CCDS70967.1

• Ensembl
  ENSMUSG00000025089 (Evidence)
• NCBI Gene
  14585

Representative Sequences			Length	Strain/Species
genomic	ENSMUSG00000025089	Ensembl Gene Model | MGI Sequence Detail	220306	C57BL/6J
transcript	ENSMUST00000026076	Ensembl | MGI Sequence Detail	4641	Not Applicable
polypeptide	ENSMUSP00000026076	Ensembl | MGI Sequence Detail	468	Not Applicable

Protein
Information

• UniProt
  11 Sequences
• Protein Ontology
  PR:000007948 GDNF family receptor alpha-1
  (term hierarchy)
• InterPro Domains
  IPR016017 GDNF/GAS1
  IPR037193 GDNF receptor alpha
  IPR003438 Glial cell line-derived neurotrophic factor receptor
  IPR003503 Glial cell line-derived neurotrophic factor receptor, alpha 1
  IPR017372 Glial cell line-derived neurotrophic factor receptor, alpha 1/2
• GlyGen
  P97785 3 sites, 1 N-linked glycan (2 sites)

Molecular
Reagents

• All nucleic 98

  cDNA 81

  Primer pair 9

  Other 8

  
  

  Microarray probesets 7

Other
Accession IDs

MGI:2147659

References

• Summaries
  All 230

  Developmental Gene Expression 132

  Diseases 2

  Gene Ontology 14

  Phenotypes 67
• Earliest
  J:43790 Molliver DC, et al., IB4-binding DRG neurons switch from NGF to GDNF dependence in early postnatal life. Neuron. 1997 Oct;19(4):849-61
• Latest
  J:363274 Kuroha K, et al., Abnormal H3K27me3 underlies degenerative spermatogonial stem cells in cryptorchid testis. Development. 2025 Jan 15;152(2):dev204239

TSS for Gfra1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr159955	Chr19:58444379-58444394 (-)	-46 bp
Tssr159954	Chr19:58444335-58444346 (-)	0 bp
Tssr159953	Chr19:58444250-58444304 (-)	64 bp
Tssr159952	Chr19:58444216-58444227 (-)	119 bp
Tssr159951	Chr19:58444040-58444054 (-)	294 bp
Tssr159950	Chr19:58444027-58444036 (-)	309 bp
Tssr159949	Chr19:58443913-58443927 (-)	421 bp
Tssr159948	Chr19:58443898-58443908 (-)	438 bp
Tssr159947	Chr19:58443847-58443890 (-)	472 bp
Tssr159946	Chr19:58443691-58443756 (-)	617 bp
Tssr159945	Chr19:58443012-58443073 (-)	1,298 bp
Tssr159944	Chr19:58442957-58442984 (-)	1,370 bp
Tssr159943	Chr19:58442922-58442944 (-)	1,408 bp
Tssr159942	Chr19:58442867-58442905 (-)	1,455 bp
Tssr159941	Chr19:58442761-58442805 (-)	1,558 bp
Tssr159940	Chr19:58442747-58442753 (-)	1,591 bp
Tssr159939	Chr19:58432014-58432020 (-)	12,324 bp
Tssr159938	Chr19:58400596-58400599 (-)	43,743 bp
Tssr159937	Chr19:58358830-58358833 (-)	85,509 bp

Gfra1 is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Afw8	Chr19, syntenic		J:99477	Authors used novel data mining tool ExQuest to identify novel candidate genes for existing diabesity QTLs. Next, candidate gene expression in the liver, adipose, and pancreas of diabesity-prone Tally Ho mice and diabesity-resistant C57BL/6J mice was assessed by quantitative PCR analysis. Several potential candidate genes, some with no previous association to diabesity QTLs, were identified. Since QTL intervals may be large and could contain hundreds or thousands of potential candidate genes, this method allows researchers to focus on those with strong potential as well as identify novel candidate genes. Potential candidate genes for Iba4 (20 cM) on mouse Chromosome 19 as identified by ExQuest are Aldh1a1 (12 cM), Aldh1a7, Vldlr (20 cM), and Plce1. Vldlr exhibits 15.6-fold increased expression in the liver of Tally Ho compared to C57BL/6 animals. For QTL Afw8 (26 cM), potential candidate genes Pi4k2a, Cpn1, and Elovl3 (47 cM) were identified. For QTLs Nobq2 (47 cM) and Bglq13 (51 cM), potential candidate genes Ins1 (49 cM), Gpam (52 cM), and Acsl5 were identified. For QTLs Tanidd1 (50 cM) and T2dm2 (53 cM), potential candidate genes Gfra1, Pnlip (29 cM), Pnliprp1 (29 cM), and Pnliprp2 were identified. Pnliprp2 exhibits 21.8-fold decreased expression in the pancreas of Tally Ho animals in response to a 4% fat diet.
Bglq13	Chr19, syntenic		J:99477	Authors used novel data mining tool ExQuest to identify novel candidate genes for existing diabesity QTLs. Next, candidate gene expression in the liver, adipose, and pancreas of diabesity-prone Tally Ho mice and diabesity-resistant C57BL/6J mice was assessed by quantitative PCR analysis. Several potential candidate genes, some with no previous association to diabesity QTLs, were identified. Since QTL intervals may be large and could contain hundreds or thousands of potential candidate genes, this method allows researchers to focus on those with strong potential as well as identify novel candidate genes. Potential candidate genes for Iba4 (20 cM) on mouse Chromosome 19 as identified by ExQuest are Aldh1a1 (12 cM), Aldh1a7, Vldlr (20 cM), and Plce1. Vldlr exhibits 15.6-fold increased expression in the liver of Tally Ho compared to C57BL/6 animals. For QTL Afw8 (26 cM), potential candidate genes Pi4k2a, Cpn1, and Elovl3 (47 cM) were identified. For QTLs Nobq2 (47 cM) and Bglq13 (51 cM), potential candidate genes Ins1 (49 cM), Gpam (52 cM), and Acsl5 were identified. For QTLs Tanidd1 (50 cM) and T2dm2 (53 cM), potential candidate genes Gfra1, Pnlip (29 cM), Pnliprp1 (29 cM), and Pnliprp2 were identified. Pnliprp2 exhibits 21.8-fold decreased expression in the pancreas of Tally Ho animals in response to a 4% fat diet.
Iba4	Chr19, 20.99 cM	Chr19:26305715-26305821	J:99477	Authors used novel data mining tool ExQuest to identify novel candidate genes for existing diabesity QTLs. Next, candidate gene expression in the liver, adipose, and pancreas of diabesity-prone Tally Ho mice and diabesity-resistant C57BL/6J mice was assessed by quantitative PCR analysis. Several potential candidate genes, some with no previous association to diabesity QTLs, were identified. Since QTL intervals may be large and could contain hundreds or thousands of potential candidate genes, this method allows researchers to focus on those with strong potential as well as identify novel candidate genes. Potential candidate genes for Iba4 (20 cM) on mouse Chromosome 19 as identified by ExQuest are Aldh1a1 (12 cM), Aldh1a7, Vldlr (20 cM), and Plce1. Vldlr exhibits 15.6-fold increased expression in the liver of Tally Ho compared to C57BL/6 animals. For QTL Afw8 (26 cM), potential candidate genes Pi4k2a, Cpn1, and Elovl3 (47 cM) were identified. For QTLs Nobq2 (47 cM) and Bglq13 (51 cM), potential candidate genes Ins1 (49 cM), Gpam (52 cM), and Acsl5 were identified. For QTLs Tanidd1 (50 cM) and T2dm2 (53 cM), potential candidate genes Gfra1, Pnlip (29 cM), Pnliprp1 (29 cM), and Pnliprp2 were identified. Pnliprp2 exhibits 21.8-fold decreased expression in the pancreas of Tally Ho animals in response to a 4% fat diet.
Nobq2	Chr19, 40.53 cM	Chr19:47897880-47897988	J:99477	Authors used novel data mining tool ExQuest to identify novel candidate genes for existing diabesity QTLs. Next, candidate gene expression in the liver, adipose, and pancreas of diabesity-prone Tally Ho mice and diabesity-resistant C57BL/6J mice was assessed by quantitative PCR analysis. Several potential candidate genes, some with no previous association to diabesity QTLs, were identified. Since QTL intervals may be large and could contain hundreds or thousands of potential candidate genes, this method allows researchers to focus on those with strong potential as well as identify novel candidate genes. Potential candidate genes for Iba4 (20 cM) on mouse Chromosome 19 as identified by ExQuest are Aldh1a1 (12 cM), Aldh1a7, Vldlr (20 cM), and Plce1. Vldlr exhibits 15.6-fold increased expression in the liver of Tally Ho compared to C57BL/6 animals. For QTL Afw8 (26 cM), potential candidate genes Pi4k2a, Cpn1, and Elovl3 (47 cM) were identified. For QTLs Nobq2 (47 cM) and Bglq13 (51 cM), potential candidate genes Ins1 (49 cM), Gpam (52 cM), and Acsl5 were identified. For QTLs Tanidd1 (50 cM) and T2dm2 (53 cM), potential candidate genes Gfra1, Pnlip (29 cM), Pnliprp1 (29 cM), and Pnliprp2 were identified. Pnliprp2 exhibits 21.8-fold decreased expression in the pancreas of Tally Ho animals in response to a 4% fat diet.
T2dm2	Chr19, 50.72 cM	Chr19:55376050-55376167	J:99477	Authors used novel data mining tool ExQuest to identify novel candidate genes for existing diabesity QTLs. Next, candidate gene expression in the liver, adipose, and pancreas of diabesity-prone Tally Ho mice and diabesity-resistant C57BL/6J mice was assessed by quantitative PCR analysis. Several potential candidate genes, some with no previous association to diabesity QTLs, were identified. Since QTL intervals may be large and could contain hundreds or thousands of potential candidate genes, this method allows researchers to focus on those with strong potential as well as identify novel candidate genes. Potential candidate genes for Iba4 (20 cM) on mouse Chromosome 19 as identified by ExQuest are Aldh1a1 (12 cM), Aldh1a7, Vldlr (20 cM), and Plce1. Vldlr exhibits 15.6-fold increased expression in the liver of Tally Ho compared to C57BL/6 animals. For QTL Afw8 (26 cM), potential candidate genes Pi4k2a, Cpn1, and Elovl3 (47 cM) were identified. For QTLs Nobq2 (47 cM) and Bglq13 (51 cM), potential candidate genes Ins1 (49 cM), Gpam (52 cM), and Acsl5 were identified. For QTLs Tanidd1 (50 cM) and T2dm2 (53 cM), potential candidate genes Gfra1, Pnlip (29 cM), Pnliprp1 (29 cM), and Pnliprp2 were identified. Pnliprp2 exhibits 21.8-fold decreased expression in the pancreas of Tally Ho animals in response to a 4% fat diet.
Tanidd1	Chr19, 48.46 cM	Chr19:53752597-53752718	J:99477	Authors used novel data mining tool ExQuest to identify novel candidate genes for existing diabesity QTLs. Next, candidate gene expression in the liver, adipose, and pancreas of diabesity-prone Tally Ho mice and diabesity-resistant C57BL/6J mice was assessed by quantitative PCR analysis. Several potential candidate genes, some with no previous association to diabesity QTLs, were identified. Since QTL intervals may be large and could contain hundreds or thousands of potential candidate genes, this method allows researchers to focus on those with strong potential as well as identify novel candidate genes. Potential candidate genes for Iba4 (20 cM) on mouse Chromosome 19 as identified by ExQuest are Aldh1a1 (12 cM), Aldh1a7, Vldlr (20 cM), and Plce1. Vldlr exhibits 15.6-fold increased expression in the liver of Tally Ho compared to C57BL/6 animals. For QTL Afw8 (26 cM), potential candidate genes Pi4k2a, Cpn1, and Elovl3 (47 cM) were identified. For QTLs Nobq2 (47 cM) and Bglq13 (51 cM), potential candidate genes Ins1 (49 cM), Gpam (52 cM), and Acsl5 were identified. For QTLs Tanidd1 (50 cM) and T2dm2 (53 cM), potential candidate genes Gfra1, Pnlip (29 cM), Pnliprp1 (29 cM), and Pnliprp2 were identified. Pnliprp2 exhibits 21.8-fold decreased expression in the pancreas of Tally Ho animals in response to a 4% fat diet.

*cM position of peak correlated region/marker