Mutagenetix > Incidental Mutation

Incidental Mutation 'R2001:Gfra1'

225992

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

040011-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R2001 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

58224036-58444341 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 58288707 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Proline at position 246 (L246P)

Ref Sequence

ENSEMBL: ENSMUSP00000130128 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000026076] [ENSMUST00000129100] [ENSMUST00000140141] [ENSMUST00000152507] [ENSMUST00000169850]

AlphaFold

P97785

Predicted Effect

probably damaging
Transcript: ENSMUST00000026076
AA Change: L246P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000026076
Gene: ENSMUSG00000025089
AA Change: L246P

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: L241P

PolyPhen 2 Score 0.686 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000117196
Gene: ENSMUSG00000025089
AA Change: L241P

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 damaging
Transcript: ENSMUST00000140141
AA Change: L246P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000123022
Gene: ENSMUSG00000025089
AA Change: L246P

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

probably damaging
Transcript: ENSMUST00000152507
AA Change: L246P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000120333
Gene: ENSMUSG00000025089
AA Change: L246P

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

probably damaging
Transcript: ENSMUST00000169850
AA Change: L246P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000130128
Gene: ENSMUSG00000025089
AA Change: L246P

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: 97.1%
20x: 94.6%

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: 96 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4932414N04Rik	T	C	2: 68,571,800 (GRCm39)	S559P	probably benign	Het
A430005L14Rik	T	A	4: 154,044,314 (GRCm39)	C42S	probably damaging	Het
Abca13	A	T	11: 9,223,967 (GRCm39)	T449S	probably benign	Het
Acvr1c	T	A	2: 58,205,987 (GRCm39)	Q41L	probably benign	Het
Adamts13	C	T	2: 26,864,002 (GRCm39)	P60L	probably benign	Het
Adamts20	T	C	15: 94,245,599 (GRCm39)	T568A	possibly damaging	Het
Ago1	T	C	4: 126,348,187 (GRCm39)	I44V	probably null	Het
Agtpbp1	TGAAGATGCATCTTGAGAAGA	TGAAGA	13: 59,623,617 (GRCm39)		probably null	Het
Ankrd28	A	T	14: 31,467,293 (GRCm39)	V39E	possibly damaging	Het
Apaf1	A	G	10: 90,897,676 (GRCm39)	V269A	possibly damaging	Het
Astn1	A	G	1: 158,348,091 (GRCm39)	N506D	probably damaging	Het
BC051019	G	A	7: 109,319,758 (GRCm39)	Q102*	probably null	Het
Bpifb5	A	G	2: 154,075,199 (GRCm39)	T376A	possibly damaging	Het
Ccdc121rt1	G	T	1: 181,338,551 (GRCm39)	Q134K	probably benign	Het
Ccl20	ATT	ATTT	1: 83,095,576 (GRCm39)		probably null	Het
Ccl6	G	T	11: 83,480,163 (GRCm39)	P68T	possibly damaging	Het
Cd300ld	A	T	11: 114,878,156 (GRCm39)	F119I	probably benign	Het
Cdk2ap2	A	G	19: 4,147,903 (GRCm39)	M57V	possibly damaging	Het
Cemip2	A	G	19: 21,779,351 (GRCm39)	D387G	probably benign	Het
Chkb	C	T	15: 89,312,969 (GRCm39)	G36E	probably damaging	Het
Col11a1	A	G	3: 113,958,942 (GRCm39)		probably null	Het
Ctla2b	T	C	13: 61,043,881 (GRCm39)	Y120C	probably damaging	Het
Ctnnd1	T	C	2: 84,450,704 (GRCm39)	N172S	probably benign	Het
Cyp2a22	G	A	7: 26,634,197 (GRCm39)	P319L	probably damaging	Het
Dcaf12	A	C	4: 41,302,804 (GRCm39)	V117G	probably damaging	Het
Ddx6	A	G	9: 44,518,831 (GRCm39)	T48A	probably benign	Het
Dgki	T	C	6: 36,842,736 (GRCm39)	D923G	possibly damaging	Het
Dhx37	G	T	5: 125,504,528 (GRCm39)	T345K	probably damaging	Het
Dhx9	A	T	1: 153,331,857 (GRCm39)	Y1370*	probably null	Het
Dnah7b	T	C	1: 46,181,247 (GRCm39)	S1045P	possibly damaging	Het
Dnmbp	G	C	19: 43,838,612 (GRCm39)	T1071S	possibly damaging	Het
Dspp	T	A	5: 104,326,425 (GRCm39)	S929R	unknown	Het
Dst	A	T	1: 34,223,144 (GRCm39)	E1625D	probably damaging	Het
Egflam	T	A	15: 7,272,048 (GRCm39)	H630L	probably benign	Het
Elane	T	C	10: 79,723,593 (GRCm39)	V186A	possibly damaging	Het
Fam209	C	A	2: 172,314,689 (GRCm39)	N59K	probably benign	Het
Gbe1	A	G	16: 70,325,814 (GRCm39)	E617G	probably damaging	Het
Get3	T	C	8: 85,751,789 (GRCm39)	S36G	probably damaging	Het
Gria2	T	C	3: 80,618,112 (GRCm39)	T308A	probably benign	Het
Grip2	A	T	6: 91,756,831 (GRCm39)	V540D	probably benign	Het
Hhipl1	A	T	12: 108,288,118 (GRCm39)	I575F	possibly damaging	Het
Hmcn1	T	A	1: 150,614,364 (GRCm39)	E1347D	possibly damaging	Het
Itga2b	C	A	11: 102,358,165 (GRCm39)	A187S	probably benign	Het
Kalrn	C	A	16: 33,848,415 (GRCm39)	R469M	probably damaging	Het
Kif23	A	T	9: 61,834,666 (GRCm39)	C426*	probably null	Het
Lck	T	C	4: 129,442,730 (GRCm39)	N475S	probably benign	Het
Leng8	A	G	7: 4,148,073 (GRCm39)	N642S	probably damaging	Het
Lingo4	T	A	3: 94,310,382 (GRCm39)	I440N	probably damaging	Het
Lrrc4	A	G	6: 28,830,904 (GRCm39)	F237S	probably damaging	Het
Magel2	G	A	7: 62,028,844 (GRCm39)	V583I	unknown	Het
Naip2	A	T	13: 100,281,096 (GRCm39)	I1316N	probably damaging	Het
Naip6	C	T	13: 100,437,237 (GRCm39)	G429S	probably benign	Het
Noct	C	T	3: 51,155,465 (GRCm39)	R78C	probably damaging	Het
Npbwr1	A	G	1: 5,987,394 (GRCm39)	V40A	possibly damaging	Het
Nsd2	A	G	5: 34,000,746 (GRCm39)	N88D	probably damaging	Het
Or1e29	T	A	11: 73,667,539 (GRCm39)	I205F	probably benign	Het
Or5ap2	T	A	2: 85,680,744 (GRCm39)	V316E	probably benign	Het
Or6c210	T	A	10: 129,496,290 (GRCm39)	I205N	probably benign	Het
Or8k28	T	C	2: 86,285,817 (GRCm39)	H266R	probably benign	Het
Pak5	T	A	2: 135,958,557 (GRCm39)	H177L	probably benign	Het
Pard3	C	T	8: 127,791,097 (GRCm39)		probably null	Het
Pde4c	A	G	8: 71,200,007 (GRCm39)		probably null	Het
Pde6h	T	A	6: 136,940,203 (GRCm39)	I63N	probably damaging	Het
Phldb2	T	C	16: 45,594,558 (GRCm39)	K916E	possibly damaging	Het
Ppig	T	C	2: 69,571,988 (GRCm39)	S236P	unknown	Het
Ptprd	T	C	4: 75,872,359 (GRCm39)	Y1370C	probably damaging	Het
Pzp	T	C	6: 128,493,083 (GRCm39)	T352A	probably benign	Het
Rab3gap1	A	G	1: 127,831,456 (GRCm39)	Y177C	possibly damaging	Het
Rasgef1a	G	A	6: 118,066,157 (GRCm39)	V457M	probably benign	Het
Scel	A	T	14: 103,848,226 (GRCm39)	T616S	possibly damaging	Het
Sel1l	A	T	12: 91,793,324 (GRCm39)	Y228*	probably null	Het
Sgms1	A	G	19: 32,137,083 (GRCm39)	V161A	possibly damaging	Het
Slfnl1	T	C	4: 120,390,424 (GRCm39)	L25P	probably benign	Het
Smad5	A	G	13: 56,885,187 (GRCm39)	T432A	probably damaging	Het
Sohlh2	T	C	3: 55,099,762 (GRCm39)		probably null	Het
Sphkap	A	T	1: 83,254,383 (GRCm39)	M835K	probably damaging	Het
Sqor	A	C	2: 122,640,018 (GRCm39)	T174P	probably damaging	Het
Stkld1	T	C	2: 26,842,759 (GRCm39)	V577A	probably damaging	Het
Sulf2	T	A	2: 165,922,773 (GRCm39)	E652D	probably benign	Het
Sycp2	T	A	2: 178,019,848 (GRCm39)	Q556L	probably benign	Het
Syk	A	G	13: 52,765,274 (GRCm39)	T134A	probably benign	Het
Tas2r122	T	A	6: 132,688,585 (GRCm39)	I103F	possibly damaging	Het
Tex10	A	G	4: 48,451,940 (GRCm39)	W729R	probably damaging	Het
Tex261	G	T	6: 83,750,713 (GRCm39)	P95T	probably damaging	Het
Tm2d2	T	C	8: 25,507,523 (GRCm39)	S47P	probably benign	Het
Tmem95	A	G	11: 69,767,817 (GRCm39)	S128P	probably damaging	Het
Tnxb	G	A	17: 34,911,553 (GRCm39)	A1619T	possibly damaging	Het
Trappc9	A	G	15: 72,929,885 (GRCm39)	I157T	probably damaging	Het
Unc13c	T	A	9: 73,390,897 (GRCm39)		probably null	Het
Upb1	A	T	10: 75,265,803 (GRCm39)	Y210F	probably damaging	Het
Urb1	T	C	16: 90,559,232 (GRCm39)	M1684V	probably benign	Het
Wnk2	G	A	13: 49,232,158 (GRCm39)	P727S	possibly damaging	Het
Zfp1004	T	A	2: 150,034,867 (GRCm39)	M396K	probably benign	Het
Zfp551	A	T	7: 12,150,276 (GRCm39)	S378T	probably damaging	Het
Zfp598	T	C	17: 24,888,898 (GRCm39)	V56A	possibly damaging	Het
Zfp945	C	T	17: 23,076,223 (GRCm39)		probably null	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
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'- ACAGATGCAGAGGTCAAACTTC -3'
(R):5'- TACAGGTCCGCCTACATCAC -3'

Sequencing Primer
(F):5'- TGCAGAGGTCAAACTTCTACTGATCC -3'
(R):5'- GCATGTCCAATGAAGTCTGC -3'

Posted On

2014-08-25