Incidental Mutation 'R4352:Gfra1'
ID 327383
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 041668-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4352 (G1)
Quality Score 225
Status Validated
Chromosome 19
Chromosomal Location 58224036-58444341 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 58255456 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Lysine at position 330 (N330K)
Ref Sequence ENSEMBL: ENSMUSP00000123022 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000026076] [ENSMUST00000129100] [ENSMUST00000140141] [ENSMUST00000152507] [ENSMUST00000169850]
AlphaFold P97785
Predicted Effect probably benign
Transcript: ENSMUST00000026076
AA Change: N330K

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
SMART Domains Protein: ENSMUSP00000026076
Gene: ENSMUSG00000025089
AA Change: N330K

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: ENSMUST00000129100
AA Change: N325K

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000117196
Gene: ENSMUSG00000025089
AA Change: N325K

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
AA Change: N330K

PolyPhen 2 Score 0.078 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000123022
Gene: ENSMUSG00000025089
AA Change: N330K

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 benign
Transcript: ENSMUST00000152507
AA Change: N330K

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
SMART Domains Protein: ENSMUSP00000120333
Gene: ENSMUSG00000025089
AA Change: N330K

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: ENSMUST00000169850
AA Change: N330K

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
SMART Domains Protein: ENSMUSP00000130128
Gene: ENSMUSG00000025089
AA Change: N330K

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 0.1094 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.1%
  • 20x: 94.6%
Validation Efficiency 96% (79/82)
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: 70 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A2ml1 C T 6: 128,557,349 (GRCm39) A115T probably benign Het
Abtb2 T A 2: 103,513,738 (GRCm39) D382E possibly damaging Het
Adamts1 T A 16: 85,599,234 (GRCm39) D122V probably benign Het
Ankrd54 A T 15: 78,939,662 (GRCm39) F176I probably benign Het
Ano3 T A 2: 110,576,239 (GRCm39) E94V possibly damaging Het
Arid1b A T 17: 5,147,859 (GRCm39) Q587L possibly damaging Het
Atg2a G A 19: 6,307,487 (GRCm39) V1474M probably benign Het
Bcl2a1d A G 9: 88,613,552 (GRCm39) V74A probably damaging Het
Bmper A G 9: 23,395,248 (GRCm39) I660V probably benign Het
Cdh20 A G 1: 104,906,814 (GRCm39) D547G probably damaging Het
Cds2 T A 2: 132,105,365 (GRCm39) M1K probably null Het
Ctr9 T A 7: 110,648,525 (GRCm39) Y722N probably damaging Het
Ddx47 C T 6: 134,995,018 (GRCm39) T161I probably benign Het
Dvl3 T C 16: 20,344,394 (GRCm39) Y257H possibly damaging Het
Dzip1 T C 14: 119,120,938 (GRCm39) D673G probably benign Het
Efcab3 T A 11: 104,630,140 (GRCm39) L957Q probably null Het
Emilin2 T C 17: 71,587,726 (GRCm39) M129V probably benign Het
Eml1 A T 12: 108,501,096 (GRCm39) probably benign Het
Espnl A T 1: 91,262,443 (GRCm39) D296V probably damaging Het
Fam161a T G 11: 22,970,798 (GRCm39) S109R possibly damaging Het
Fat3 T G 9: 16,158,074 (GRCm39) T1179P possibly damaging Het
Gfy T C 7: 44,827,040 (GRCm39) E352G probably benign Het
Gm20775 A T Y: 10,641,648 (GRCm39) noncoding transcript Het
Gm5885 T A 6: 133,508,152 (GRCm39) noncoding transcript Het
Gpatch11 T C 17: 79,148,446 (GRCm39) L128P probably damaging Het
H2-Q1 A G 17: 35,539,919 (GRCm39) N63D possibly damaging Het
Itgb2 A T 10: 77,392,001 (GRCm39) N358I probably benign Het
Jmjd1c A G 10: 67,080,588 (GRCm39) T2247A probably damaging Het
Kcnma1 T A 14: 23,361,720 (GRCm39) K1036I probably damaging Het
Llgl1 C T 11: 60,600,394 (GRCm39) P581L probably benign Het
Lrch1 G T 14: 75,056,018 (GRCm39) S278R probably damaging Het
Lrp2 C A 2: 69,262,526 (GRCm39) probably null Het
Lyn G A 4: 3,789,796 (GRCm39) R443H probably damaging Het
Mecom C A 3: 30,020,887 (GRCm39) V452L possibly damaging Het
Mpzl1 G A 1: 165,433,376 (GRCm39) Q36* probably null Het
Msantd5 A G 11: 51,125,646 (GRCm39) N190D possibly damaging Het
Npr2 T C 4: 43,646,592 (GRCm39) S647P probably damaging Het
Nrp2 A G 1: 62,777,576 (GRCm39) D127G probably damaging Het
Otogl A T 10: 107,705,396 (GRCm39) C644S probably damaging Het
Pabpc4 C T 4: 123,184,060 (GRCm39) T191I probably damaging Het
Paqr3 T C 5: 97,247,455 (GRCm39) T218A probably benign Het
Pcdh7 C T 5: 57,879,361 (GRCm39) S972L possibly damaging Het
Pcnx2 T C 8: 126,489,590 (GRCm39) H1668R probably damaging Het
Prb1b T G 6: 132,290,624 (GRCm39) Y25S unknown Het
Ralb A G 1: 119,411,282 (GRCm39) M19T probably benign Het
Rcan1 A G 16: 92,190,384 (GRCm39) I185T probably benign Het
Rnf38 A T 4: 44,149,100 (GRCm39) N82K possibly damaging Het
Rock1 T A 18: 10,079,237 (GRCm39) Q1077L probably damaging Het
Sesn3 C T 9: 14,231,669 (GRCm39) A200V probably damaging Het
Shh T C 5: 28,663,187 (GRCm39) E327G probably benign Het
Shmt2 G A 10: 127,354,686 (GRCm39) A333V probably damaging Het
Slc15a2 T A 16: 36,592,390 (GRCm39) I256F probably benign Het
Sptbn5 T C 2: 119,913,680 (GRCm39) noncoding transcript Het
Sst A G 16: 23,708,565 (GRCm39) S89P probably damaging Het
Taf10 A G 7: 105,392,614 (GRCm39) probably benign Het
Tas2r139 T A 6: 42,118,689 (GRCm39) W274R probably damaging Het
Tbc1d20 T A 2: 152,150,114 (GRCm39) probably benign Het
Tbc1d5 A G 17: 51,089,429 (GRCm39) S584P probably damaging Het
Tcstv1a T C 13: 120,355,407 (GRCm39) D75G probably damaging Het
Tex10 T G 4: 48,452,039 (GRCm39) T696P possibly damaging Het
Tgfbr1 T C 4: 47,402,863 (GRCm39) F206S probably damaging Het
Tmem241 A T 18: 12,246,496 (GRCm39) H51Q probably benign Het
Trim5 A T 7: 103,926,015 (GRCm39) V182D probably damaging Het
Ttn A T 2: 76,641,587 (GRCm39) L5176Q possibly damaging Het
Txnl1 A G 18: 63,804,750 (GRCm39) V248A possibly damaging Het
Ubr5 A G 15: 38,041,817 (GRCm39) V204A probably benign Het
Ugp2 C T 11: 21,279,026 (GRCm39) V387I probably damaging Het
Unc45b G A 11: 82,804,035 (GRCm39) D71N probably damaging Het
Usp34 A T 11: 23,270,727 (GRCm39) Y37F possibly damaging Het
Zfp943 A T 17: 22,212,104 (GRCm39) I397F 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
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
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'- ATCACGTGTGTGGTTCCCTG -3'
(R):5'- GGTCATAGAAGTGTCCGTGTC -3'

Sequencing Primer
(F):5'- GCTGTGTCACTGAGCATACC -3'
(R):5'- AGTGTCCGTGTCAACATAGG -3'
Posted On 2015-07-07