Incidental Mutation 'R2866:Gfra1'
| ID |
253305 |
| 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 |
040455-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R2866 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
19 |
| Chromosomal Location |
58224036-58444341 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 58227739 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Alanine to Threonine
at position 395
(A395T)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000117196
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000026076]
[ENSMUST00000129100]
[ENSMUST00000140141]
[ENSMUST00000152507]
[ENSMUST00000169850]
|
| AlphaFold |
P97785 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000026076
AA Change: A400T
PolyPhen 2
Score 0.857 (Sensitivity: 0.83; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000026076
Gene: ENSMUSG00000025089
AA Change: A400T
| Domain | Start | End | E-Value | Type |
|---|
|
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: A395T
PolyPhen 2
Score 0.933 (Sensitivity: 0.80; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000117196
Gene: ENSMUSG00000025089
AA Change: A395T
| Domain | Start | End | E-Value | Type |
|---|
|
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
| Domain | Start | End | E-Value | Type |
|---|
|
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: A400T
PolyPhen 2
Score 0.857 (Sensitivity: 0.83; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000120333
Gene: ENSMUSG00000025089
AA Change: A400T
| Domain | Start | End | E-Value | Type |
|---|
|
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: A400T
PolyPhen 2
Score 0.857 (Sensitivity: 0.83; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000130128
Gene: ENSMUSG00000025089
AA Change: A400T
| Domain | Start | End | E-Value | Type |
|---|
|
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: 99.2%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.2%
|
| 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: 43 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Atmin |
T |
A |
8: 117,683,112 (GRCm39) |
D257E |
probably benign |
Het |
| Best1 |
T |
C |
19: 9,963,585 (GRCm39) |
E532G |
probably benign |
Het |
| Cenpj |
T |
C |
14: 56,789,637 (GRCm39) |
H804R |
probably benign |
Het |
| Clec2g |
T |
C |
6: 128,925,719 (GRCm39) |
S43P |
probably benign |
Het |
| Col8a2 |
A |
G |
4: 126,204,992 (GRCm39) |
|
probably benign |
Het |
| Cpz |
T |
C |
5: 35,659,705 (GRCm39) |
K647E |
probably benign |
Het |
| Csmd2 |
T |
C |
4: 128,308,185 (GRCm39) |
|
probably null |
Het |
| Ctss |
A |
G |
3: 95,452,717 (GRCm39) |
K166R |
probably benign |
Het |
| Cyp2c23 |
T |
C |
19: 43,993,885 (GRCm39) |
R494G |
probably damaging |
Het |
| Cyp2c68 |
A |
G |
19: 39,677,589 (GRCm39) |
I467T |
probably damaging |
Het |
| Dcaf11 |
A |
T |
14: 55,803,202 (GRCm39) |
T299S |
possibly damaging |
Het |
| Dennd1b |
A |
G |
1: 139,098,019 (GRCm39) |
S762G |
possibly damaging |
Het |
| Epb42 |
C |
T |
2: 120,856,402 (GRCm39) |
A381T |
possibly damaging |
Het |
| Fhad1 |
A |
G |
4: 141,648,099 (GRCm39) |
Y256H |
probably benign |
Het |
| Gm10323 |
C |
A |
13: 67,002,574 (GRCm39) |
C55F |
probably benign |
Het |
| Greb1 |
T |
C |
12: 16,749,551 (GRCm39) |
S1092G |
probably damaging |
Het |
| Grid1 |
A |
T |
14: 35,284,516 (GRCm39) |
D753V |
probably damaging |
Het |
| Grin2b |
A |
G |
6: 135,710,637 (GRCm39) |
F970L |
probably damaging |
Het |
| Kcnma1 |
A |
T |
14: 23,423,275 (GRCm39) |
N682K |
probably benign |
Het |
| Lat2 |
T |
A |
5: 134,634,798 (GRCm39) |
D114V |
probably damaging |
Het |
| Lcat |
C |
T |
8: 106,666,511 (GRCm39) |
C337Y |
probably damaging |
Het |
| Mapk10 |
C |
T |
5: 103,186,548 (GRCm39) |
D25N |
probably benign |
Het |
| Mroh7 |
C |
T |
4: 106,548,287 (GRCm39) |
G1064R |
probably damaging |
Het |
| Muc21 |
T |
C |
17: 35,930,599 (GRCm39) |
|
probably benign |
Het |
| Or10h5 |
T |
A |
17: 33,435,252 (GRCm39) |
H22L |
probably benign |
Het |
| Or51ah3 |
A |
T |
7: 103,210,064 (GRCm39) |
I127F |
probably damaging |
Het |
| Or5p5 |
T |
A |
7: 107,414,126 (GRCm39) |
C112S |
probably benign |
Het |
| Or8k39 |
A |
T |
2: 86,563,773 (GRCm39) |
F61Y |
possibly damaging |
Het |
| Polr1has |
A |
T |
17: 37,276,052 (GRCm39) |
R211S |
possibly damaging |
Het |
| Psg27 |
T |
A |
7: 18,295,818 (GRCm39) |
D209V |
probably benign |
Het |
| Ptgir |
A |
G |
7: 16,640,794 (GRCm39) |
M29V |
possibly damaging |
Het |
| Pzp |
A |
G |
6: 128,502,227 (GRCm39) |
S41P |
possibly damaging |
Het |
| Rab23 |
A |
T |
1: 33,777,376 (GRCm39) |
K163N |
possibly damaging |
Het |
| Rilpl2 |
T |
C |
5: 124,615,898 (GRCm39) |
D84G |
probably damaging |
Het |
| Sorl1 |
A |
G |
9: 41,881,077 (GRCm39) |
I2148T |
probably benign |
Het |
| Tead1 |
A |
G |
7: 112,358,694 (GRCm39) |
E2G |
probably damaging |
Het |
| Tigd4 |
A |
G |
3: 84,501,259 (GRCm39) |
N59D |
possibly damaging |
Het |
| Tmprss15 |
T |
A |
16: 78,832,121 (GRCm39) |
D345V |
possibly damaging |
Het |
| Togaram2 |
T |
C |
17: 72,016,592 (GRCm39) |
S649P |
probably benign |
Het |
| Ucp2 |
T |
C |
7: 100,146,459 (GRCm39) |
V95A |
probably benign |
Het |
| Usp17lb |
T |
C |
7: 104,489,955 (GRCm39) |
D323G |
probably damaging |
Het |
| Zfp677 |
A |
T |
17: 21,617,518 (GRCm39) |
K192* |
probably null |
Het |
| Zmym2 |
T |
A |
14: 57,165,705 (GRCm39) |
I676K |
probably damaging |
Het |
|
| Other mutations in Gfra1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH 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 |
|
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'- GCTGATGAGAACTTTTCTGGATC -3'
(R):5'- GAGTCACCCCTTCAAAGCTC -3'
Sequencing Primer
(F):5'- CTGGATCCAAGACACTATTGGTC -3'
(R):5'- TACCAGTGACAGGTAGCTGCTG -3'
|
| Posted On |
2014-12-04 |
Incidental Mutation