Incidental Mutation 'R9659:Gfra1'
ID 727483
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
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R9659 (G1)
Quality Score 225.009
Status Not validated
Chromosome 19
Chromosomal Location 58224036-58444341 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 58441652 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Threonine at position 93 (M93T)
Ref Sequence ENSEMBL: ENSMUSP00000026076 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000026076] [ENSMUST00000123957] [ENSMUST00000129100] [ENSMUST00000131877] [ENSMUST00000135730] [ENSMUST00000138530] [ENSMUST00000140141] [ENSMUST00000152507] [ENSMUST00000169850]
AlphaFold P97785
Predicted Effect probably damaging
Transcript: ENSMUST00000026076
AA Change: M93T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000026076
Gene: ENSMUSG00000025089
AA Change: M93T

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 probably benign
Transcript: ENSMUST00000123957
Predicted Effect possibly damaging
Transcript: ENSMUST00000129100
AA Change: M93T

PolyPhen 2 Score 0.937 (Sensitivity: 0.80; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000117196
Gene: ENSMUSG00000025089
AA Change: M93T

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: ENSMUST00000131877
Predicted Effect probably benign
Transcript: ENSMUST00000135730
Predicted Effect probably benign
Transcript: ENSMUST00000138530
SMART Domains Protein: ENSMUSP00000115239
Gene: ENSMUSG00000025089

DomainStartEndE-ValueType
signal peptide 1 24 N/A INTRINSIC
Blast:GDNF 29 54 2e-10 BLAST
Predicted Effect probably damaging
Transcript: ENSMUST00000140141
AA Change: M93T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000123022
Gene: ENSMUSG00000025089
AA Change: M93T

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 probably damaging
Transcript: ENSMUST00000152507
AA Change: M93T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000120333
Gene: ENSMUSG00000025089
AA Change: M93T

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 probably damaging
Transcript: ENSMUST00000169850
AA Change: M93T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000130128
Gene: ENSMUSG00000025089
AA Change: M93T

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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.2%
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: 61 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A330070K13Rik T C 5: 130,407,876 (GRCm39) I112V unknown Het
Adcy7 A G 8: 89,045,733 (GRCm39) T572A probably benign Het
Atad5 G T 11: 79,980,542 (GRCm39) probably benign Het
C2cd2 A G 16: 97,723,473 (GRCm39) S15P possibly damaging Het
Cabp1 T C 5: 115,311,187 (GRCm39) D289G possibly damaging Het
Ccdc14 A G 16: 34,541,913 (GRCm39) I545V probably damaging Het
Cep295 C A 9: 15,233,846 (GRCm39) A2317S probably benign Het
Cerkl T C 2: 79,223,322 (GRCm39) D133G possibly damaging Het
Cited4 T G 4: 120,524,543 (GRCm39) C182G probably damaging Het
Col6a5 T A 9: 105,811,034 (GRCm39) K828N unknown Het
Ear2 A G 14: 44,340,705 (GRCm39) Y121C probably damaging Het
Ect2l C T 10: 18,041,347 (GRCm39) C369Y possibly damaging Het
Elapor1 G A 3: 108,377,297 (GRCm39) T387I possibly damaging Het
Ep300 A G 15: 81,505,273 (GRCm39) Y631C unknown Het
Ephb4 T G 5: 137,363,743 (GRCm39) Y583D probably damaging Het
Fbn2 C G 18: 58,342,654 (GRCm39) R75P probably damaging Het
Gabra2 T C 5: 71,192,140 (GRCm39) D63G probably benign Het
Gm21886 AGAGGCCTGCAGACAGTAGGTGCTCACTAGGGCCTGCAGACAGCAGGTGCTCACTGAGGCCTG AGAGGCCTG 18: 80,132,776 (GRCm39) probably benign Het
Gm3604 A T 13: 62,519,724 (GRCm39) H10Q possibly damaging Het
Helz2 T C 2: 180,882,025 (GRCm39) D256G probably benign Het
Herc1 A C 9: 66,307,185 (GRCm39) I1002L probably benign Het
Hpgd C G 8: 56,772,075 (GRCm39) C182W probably damaging Het
Htr5b A G 1: 121,455,428 (GRCm39) L164P possibly damaging Het
Kmo T C 1: 175,486,085 (GRCm39) F403L probably damaging Het
Ly75 C A 2: 60,168,665 (GRCm39) D748Y probably damaging Het
Mcm5 C T 8: 75,844,168 (GRCm39) S313F probably benign Het
Mipep A G 14: 61,083,893 (GRCm39) T595A probably damaging Het
Muc6 T C 7: 141,232,100 (GRCm39) D968G probably damaging Het
Myo18b T C 5: 113,022,382 (GRCm39) T337A unknown Het
Nlrp1b T A 11: 71,073,132 (GRCm39) Q237L possibly damaging Het
Nr1h4 A G 10: 89,314,638 (GRCm39) probably null Het
Nxph1 A G 6: 9,247,418 (GRCm39) T130A probably damaging Het
Or10al6 T G 17: 38,082,880 (GRCm39) F112C probably damaging Het
Or1l4 T A 2: 37,091,897 (GRCm39) C215S possibly damaging Het
Or4m1 A G 14: 50,558,181 (GRCm39) F37S probably benign Het
Or5p4 T C 7: 107,680,745 (GRCm39) V248A probably damaging Het
Or8g21 A G 9: 38,906,296 (GRCm39) V145A possibly damaging Het
Pcsk5 A G 19: 17,455,245 (GRCm39) Y1062H probably benign Het
Plch1 T C 3: 63,681,136 (GRCm39) I164V probably benign Het
Plekhh2 T A 17: 84,854,892 (GRCm39) M42K possibly damaging Het
Polr2a T C 11: 69,625,654 (GRCm39) Y1832C unknown Het
Prpf4 G A 4: 62,334,296 (GRCm39) probably null Het
Psg16 T C 7: 16,824,524 (GRCm39) S12P possibly damaging Het
Ptpn14 T A 1: 189,587,174 (GRCm39) M528K probably benign Het
Rb1cc1 T A 1: 6,318,673 (GRCm39) H697Q probably benign Het
Reg3a T G 6: 78,360,574 (GRCm39) C171G possibly damaging Het
Slc22a26 G A 19: 7,763,798 (GRCm39) P412S probably benign Het
Spata31e5 G T 1: 28,816,536 (GRCm39) H499N probably benign Het
Tcstv2a T A 13: 120,725,754 (GRCm39) D139E probably damaging Het
Tlk2 T C 11: 105,131,263 (GRCm39) I203T probably benign Het
Tmem120b T G 5: 123,253,788 (GRCm39) H279Q probably damaging Het
Trip4 T C 9: 65,740,702 (GRCm39) E535G probably benign Het
Ttn C T 2: 76,715,357 (GRCm39) E7912K unknown Het
Ubr5 A T 15: 37,984,254 (GRCm39) L2298I Het
Utp20 A G 10: 88,653,171 (GRCm39) L303P probably damaging Het
Vcan A G 13: 89,839,860 (GRCm39) Y1895H probably damaging Het
Vmn2r2 T C 3: 64,041,942 (GRCm39) N258D possibly damaging Het
Wdr20rt A T 12: 65,273,343 (GRCm39) S269C probably damaging Het
Zfand4 T G 6: 116,282,588 (GRCm39) Y54D probably damaging Het
Zfp82 C T 7: 29,755,963 (GRCm39) R373H probably damaging Het
Zmiz2 A G 11: 6,346,814 (GRCm39) E141G probably benign 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
R1344:Gfra1 UTSW 19 58,226,849 (GRCm39) missense possibly damaging 0.88
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
R9788:Gfra1 UTSW 19 58,441,652 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TAGAGGCCAATGAAAGGTCCTC -3'
(R):5'- GTGTGAAAGCCAGTGATCAGTG -3'

Sequencing Primer
(F):5'- TGAAAGGTCCTCATTCCGCAG -3'
(R):5'- CCAGTGATCAGTGCCTGAAG -3'
Posted On 2022-10-06