Incidental Mutation 'R1344:Gfra1'
ID 200785
Institutional Source Beutler Lab
Gene Symbol Gfra1
Ensembl Gene ENSMUSG00000025089
Gene Name glial cell line derived neurotrophic factor family receptor alpha 1
Synonyms GFR alpha-1, GDNFR-alpha
MMRRC Submission 039409-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1344 (G1)
Quality Score 225
Status Not validated
Chromosome 19
Chromosomal Location 58224036-58444341 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to C at 58226849 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Alanine at position 461 (S461A)
Ref Sequence ENSEMBL: ENSMUSP00000130128 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000026076] [ENSMUST00000129100] [ENSMUST00000140141] [ENSMUST00000152507] [ENSMUST00000169850]
AlphaFold P97785
Predicted Effect possibly damaging
Transcript: ENSMUST00000026076
AA Change: S461A

PolyPhen 2 Score 0.875 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000026076
Gene: ENSMUSG00000025089
AA Change: S461A

DomainStartEndE-ValueType
signal peptide 1 24 N/A INTRINSIC
GDNF 29 111 1.96e-13 SMART
GDNF 154 233 6.55e-24 SMART
GDNF 243 337 1.62e-28 SMART
low complexity region 362 370 N/A INTRINSIC
low complexity region 455 465 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000129100
AA Change: S456A

PolyPhen 2 Score 0.461 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000117196
Gene: ENSMUSG00000025089
AA Change: S456A

DomainStartEndE-ValueType
signal peptide 1 24 N/A INTRINSIC
GDNF 29 111 1.96e-13 SMART
GDNF 149 228 6.55e-24 SMART
GDNF 238 332 1.62e-28 SMART
low complexity region 357 365 N/A INTRINSIC
low complexity region 450 460 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000140141
SMART Domains Protein: ENSMUSP00000123022
Gene: ENSMUSG00000025089

DomainStartEndE-ValueType
signal peptide 1 24 N/A INTRINSIC
GDNF 29 111 1.96e-13 SMART
GDNF 154 233 6.55e-24 SMART
GDNF 243 337 1.62e-28 SMART
low complexity region 362 370 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000143595
Predicted Effect possibly damaging
Transcript: ENSMUST00000152507
AA Change: S461A

PolyPhen 2 Score 0.875 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000120333
Gene: ENSMUSG00000025089
AA Change: S461A

DomainStartEndE-ValueType
signal peptide 1 24 N/A INTRINSIC
GDNF 29 111 1.96e-13 SMART
GDNF 154 233 6.55e-24 SMART
GDNF 243 337 1.62e-28 SMART
low complexity region 362 370 N/A INTRINSIC
low complexity region 455 465 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000169850
AA Change: S461A

PolyPhen 2 Score 0.875 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000130128
Gene: ENSMUSG00000025089
AA Change: S461A

DomainStartEndE-ValueType
signal peptide 1 24 N/A INTRINSIC
GDNF 29 111 1.96e-13 SMART
GDNF 154 233 6.55e-24 SMART
GDNF 243 337 1.62e-28 SMART
low complexity region 362 370 N/A INTRINSIC
low complexity region 455 465 N/A INTRINSIC
Meta Mutation Damage Score 0.0695 question?
Coding Region Coverage
  • 1x: 97.4%
  • 3x: 96.8%
  • 10x: 95.2%
  • 20x: 92.2%
Validation Efficiency
MGI Phenotype FUNCTION: This gene encodes a transmembrane protein that functions as the receptor for glial cell line derived neurotrophic factor (GDNF). The encoded protein undergoes proteolytic processing to generate a glycosylphosphatidylinositol-anchored cell surface coreceptor that forms a complex with the Ret tyrosine kinase in GDNF signaling pathway. Mice lacking the encoded protein exhibit deficits in the kidneys, the enteric nervous system, and spinal motor and sensory neurons similar mice deficient in GDNF or Ret. [provided by RefSeq, Jul 2016]
PHENOTYPE: Homozygotes for targeted null mutations lack kidneys and enteric neurons resulting in neonatal lethality. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 79 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
5730596B20Rik T G 6: 52,156,131 (GRCm39) probably benign Het
Aco1 T C 4: 40,179,008 (GRCm39) Y336H probably damaging Het
Adamts12 T A 15: 11,286,890 (GRCm39) W832R probably damaging Het
Asxl2 A G 12: 3,543,790 (GRCm39) K320E probably damaging Het
Atrnl1 G A 19: 57,924,137 (GRCm39) probably null Het
B4galnt2 A C 11: 95,760,181 (GRCm39) I282S probably benign Het
Bcl2l13 T C 6: 120,853,288 (GRCm39) I191T probably benign Het
Bltp3a A G 17: 28,113,551 (GRCm39) K1241R probably benign Het
Cd101 A T 3: 100,926,091 (GRCm39) Y209* probably null Het
Cd109 A T 9: 78,579,832 (GRCm39) probably null Het
Cdc34 G A 10: 79,521,134 (GRCm39) A128T probably damaging Het
Cdk12 T A 11: 98,132,611 (GRCm39) S1013R unknown Het
Cntd1 T A 11: 101,176,566 (GRCm39) L221Q possibly damaging Het
Cntn4 G A 6: 106,321,831 (GRCm39) probably null Het
Col12a1 T A 9: 79,606,837 (GRCm39) K529* probably null Het
Col17a1 T A 19: 47,659,944 (GRCm39) D336V probably damaging Het
Creb3l4 A G 3: 90,146,045 (GRCm39) I193T possibly damaging Het
Cyp2d10 A T 15: 82,290,106 (GRCm39) probably null Het
Dcun1d3 A G 7: 119,457,158 (GRCm39) F185L probably damaging Het
Dlec1 G A 9: 118,959,085 (GRCm39) E910K probably benign Het
Dnajc19 T A 3: 34,112,161 (GRCm39) N128I probably damaging Het
Dusp1 A G 17: 26,727,293 (GRCm39) V2A probably benign Het
Eea1 G A 10: 95,830,861 (GRCm39) probably null Het
Elf1 T C 14: 79,798,215 (GRCm39) V34A probably damaging Het
Extl1 T C 4: 134,086,552 (GRCm39) D501G probably damaging Het
Fcgr2b T C 1: 170,788,650 (GRCm39) Y319C probably damaging Het
Fhip2a G A 19: 57,359,594 (GRCm39) A45T possibly damaging Het
Fxr2 A G 11: 69,539,710 (GRCm39) H247R possibly damaging Het
Gask1a A T 9: 121,807,452 (GRCm39) H532L probably damaging Het
Gli2 T G 1: 118,769,666 (GRCm39) I629L probably damaging Het
Gpx3 G A 11: 54,800,422 (GRCm39) V207I probably damaging Het
Helz2 T C 2: 180,879,389 (GRCm39) D743G possibly damaging Het
Hormad2 A G 11: 4,359,005 (GRCm39) probably null Het
Ifitm1 C T 7: 140,548,263 (GRCm39) T32M probably benign Het
Iqca1 C A 1: 90,070,453 (GRCm39) G133V probably null Het
Lrit2 A G 14: 36,790,513 (GRCm39) N64S probably benign Het
Lsm14a A T 7: 34,052,982 (GRCm39) D322E probably damaging Het
Macf1 T G 4: 123,327,246 (GRCm39) R4752S probably damaging Het
Mark3 T C 12: 111,594,271 (GRCm39) I307T possibly damaging Het
Mpdz T A 4: 81,226,556 (GRCm39) T1360S probably benign Het
Mtif2 G A 11: 29,495,002 (GRCm39) V701I probably benign Het
Myh3 A G 11: 66,983,158 (GRCm39) E895G probably benign Het
Ncan A C 8: 70,560,819 (GRCm39) I716R probably benign Het
Ncor2 C T 5: 125,102,510 (GRCm39) R1867K probably damaging Het
Oas1d C T 5: 121,052,959 (GRCm39) L5F probably damaging Het
Or10s1 T A 9: 39,985,768 (GRCm39) L59H probably damaging Het
Or11h4b T A 14: 50,918,315 (GRCm39) M259L probably benign Het
Or13a17 T C 7: 140,271,712 (GRCm39) V298A probably damaging Het
Or3a4 A T 11: 73,945,038 (GRCm39) C182* probably null Het
Otog G T 7: 45,924,039 (GRCm39) A1133S probably damaging Het
Oxtr C T 6: 112,454,138 (GRCm39) R42Q probably benign Het
Pcdhb2 G A 18: 37,428,710 (GRCm39) V228I possibly damaging Het
Pdcd11 A G 19: 47,118,516 (GRCm39) D1794G probably damaging Het
Pde1c T C 6: 56,338,752 (GRCm39) I27V probably benign Het
Pde4d C A 13: 110,086,921 (GRCm39) S609* probably null Het
Piezo2 T A 18: 63,154,325 (GRCm39) I2485F probably damaging Het
Plekhd1 A G 12: 80,739,659 (GRCm39) T3A probably benign Het
Plscr1 C T 9: 92,141,357 (GRCm39) T15I unknown Het
Rd3 T C 1: 191,717,262 (GRCm39) *106R probably null Het
Rnf125 A G 18: 21,114,288 (GRCm39) I97V possibly damaging Het
Sec24b T C 3: 129,801,072 (GRCm39) N408S probably damaging Het
Sf3b3 G C 8: 111,564,935 (GRCm39) A291G probably damaging Het
Simc1 T C 13: 54,698,292 (GRCm39) V403A probably damaging Het
Slc38a9 T C 13: 112,826,714 (GRCm39) C151R probably benign Het
Slco1a8 A G 6: 141,931,344 (GRCm39) S474P probably damaging Het
Slitrk5 A G 14: 111,917,821 (GRCm39) S482G probably benign Het
Smyd1 G A 6: 71,239,151 (GRCm39) T13I probably benign Het
Speer4a3 T A 5: 26,158,107 (GRCm39) T82S probably benign Het
Stoml2 T A 4: 43,028,197 (GRCm39) I344F probably benign Het
Tet1 C T 10: 62,650,300 (GRCm39) R1636H probably damaging Het
Thap12 A G 7: 98,366,037 (GRCm39) D735G probably damaging Het
Tnip3 T C 6: 65,574,413 (GRCm39) V88A probably benign Het
Ttn A G 2: 76,565,755 (GRCm39) V28199A possibly damaging Het
Ube3b T C 5: 114,556,636 (GRCm39) F989S probably damaging Het
Ubox5 A G 2: 130,442,210 (GRCm39) L159P probably damaging Het
Uevld A T 7: 46,587,758 (GRCm39) V314E possibly damaging Het
Urb1 T C 16: 90,566,354 (GRCm39) M1478V probably damaging Het
Ust C A 10: 8,173,954 (GRCm39) V184F possibly damaging Het
Wdr95 G A 5: 149,511,563 (GRCm39) C421Y probably damaging Het
Other mutations in Gfra1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00820:Gfra1 APN 19 58,252,337 (GRCm39) splice site probably benign
IGL01633:Gfra1 APN 19 58,255,479 (GRCm39) missense probably benign 0.41
IGL02675:Gfra1 APN 19 58,441,787 (GRCm39) missense probably damaging 1.00
IGL02676:Gfra1 APN 19 58,441,787 (GRCm39) missense probably damaging 1.00
IGL02677:Gfra1 APN 19 58,441,787 (GRCm39) missense probably damaging 1.00
IGL02723:Gfra1 APN 19 58,441,683 (GRCm39) missense probably benign 0.00
3-1:Gfra1 UTSW 19 58,286,999 (GRCm39) intron probably benign
R0245:Gfra1 UTSW 19 58,288,986 (GRCm39) missense possibly damaging 0.72
R0652:Gfra1 UTSW 19 58,288,986 (GRCm39) missense possibly damaging 0.72
R0697:Gfra1 UTSW 19 58,258,555 (GRCm39) missense probably benign
R0699:Gfra1 UTSW 19 58,258,555 (GRCm39) missense probably benign
R1418:Gfra1 UTSW 19 58,226,849 (GRCm39) missense possibly damaging 0.88
R1468:Gfra1 UTSW 19 58,440,407 (GRCm39) missense probably benign 0.00
R1468:Gfra1 UTSW 19 58,440,407 (GRCm39) missense probably benign 0.00
R2001:Gfra1 UTSW 19 58,288,707 (GRCm39) missense probably damaging 1.00
R2866:Gfra1 UTSW 19 58,227,739 (GRCm39) missense possibly damaging 0.93
R3416:Gfra1 UTSW 19 58,255,544 (GRCm39) missense probably damaging 1.00
R4352:Gfra1 UTSW 19 58,255,456 (GRCm39) missense probably benign 0.08
R4564:Gfra1 UTSW 19 58,227,682 (GRCm39) splice site probably null
R4727:Gfra1 UTSW 19 58,252,386 (GRCm39) missense probably damaging 0.96
R4755:Gfra1 UTSW 19 58,441,676 (GRCm39) missense probably damaging 1.00
R4914:Gfra1 UTSW 19 58,255,522 (GRCm39) missense probably damaging 1.00
R4915:Gfra1 UTSW 19 58,255,522 (GRCm39) missense probably damaging 1.00
R4917:Gfra1 UTSW 19 58,255,522 (GRCm39) missense probably damaging 1.00
R5813:Gfra1 UTSW 19 58,227,687 (GRCm39) missense probably benign
R6225:Gfra1 UTSW 19 58,226,830 (GRCm39) missense probably damaging 1.00
R7023:Gfra1 UTSW 19 58,442,764 (GRCm39) missense probably damaging 1.00
R7485:Gfra1 UTSW 19 58,288,744 (GRCm39) missense probably damaging 1.00
R7624:Gfra1 UTSW 19 58,226,878 (GRCm39) missense probably benign
R7718:Gfra1 UTSW 19 58,441,889 (GRCm39) missense possibly damaging 0.69
R9659:Gfra1 UTSW 19 58,441,652 (GRCm39) missense probably damaging 1.00
R9788:Gfra1 UTSW 19 58,441,652 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CCAGGTTACAAACAGTCCCCTGAAG -3'
(R):5'- CCAGCTTGTTGGGAAGGAGCTATC -3'

Sequencing Primer
(F):5'- CAGTTCTTCAACAGAAGCCTGTG -3'
(R):5'- ACGGGTAAAATCCAACCTGAG -3'
Posted On 2014-05-23