Mutagenetix > Incidental Mutation

Incidental Mutation 'R7023:Gfra1'

545817

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

045124-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7023 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

58224036-58444341 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 58442764 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Glutamine at position 6 (L6Q)

Ref Sequence

ENSEMBL: ENSMUSP00000130128 (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: L6Q

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000026076
Gene: ENSMUSG00000025089
AA Change: L6Q

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: ENSMUST00000123957
AA Change: L6Q

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

Predicted Effect

probably damaging
Transcript: ENSMUST00000129100
AA Change: L6Q

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000117196
Gene: ENSMUSG00000025089
AA Change: L6Q

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: ENSMUST00000131877
AA Change: L6Q

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

Predicted Effect

probably damaging
Transcript: ENSMUST00000135730
AA Change: L6Q

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

Predicted Effect

probably damaging
Transcript: ENSMUST00000138530
AA Change: L6Q

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000115239
Gene: ENSMUSG00000025089
AA Change: L6Q

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
Blast:GDNF	29	54	2e-10	BLAST

Predicted Effect

probably damaging
Transcript: ENSMUST00000140141
AA Change: L6Q

PolyPhen 2 Score 0.986 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000123022
Gene: ENSMUSG00000025089
AA Change: L6Q

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: L6Q

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000120333
Gene: ENSMUSG00000025089
AA Change: L6Q

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: L6Q

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000130128
Gene: ENSMUSG00000025089
AA Change: L6Q

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: 100.0%
3x: 100.0%
10x: 99.7%
20x: 98.9%

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: 85 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4833420G17Rik	A	G	13: 119,610,443 (GRCm39)	H372R	probably benign	Het
4933405O20Rik	T	C	7: 50,250,001 (GRCm39)	I345T	probably damaging	Het
4933427D14Rik	A	G	11: 72,069,229 (GRCm39)		probably null	Het
6430548M08Rik	T	C	8: 120,872,096 (GRCm39)	V8A	probably damaging	Het
Adam2	A	T	14: 66,280,505 (GRCm39)	D501E	probably benign	Het
Agbl3	T	C	6: 34,791,704 (GRCm39)	V602A	probably benign	Het
Akap12	T	C	10: 4,306,895 (GRCm39)	M1235T	probably benign	Het
Arid5a	G	A	1: 36,356,631 (GRCm39)		probably benign	Het
Asxl1	T	A	2: 153,242,469 (GRCm39)	D1006E	probably benign	Het
AY074887	T	C	9: 54,858,149 (GRCm39)		probably benign	Het
Btbd9	T	A	17: 30,746,546 (GRCm39)	R93S	probably benign	Het
Cabp2	A	T	19: 4,132,658 (GRCm39)		probably null	Het
Cacna1e	T	C	1: 154,601,439 (GRCm39)	D76G	probably null	Het
Cd177	A	G	7: 24,459,187 (GRCm39)	I74T	probably benign	Het
Chchd1	G	A	14: 20,753,310 (GRCm39)		probably benign	Het
Col28a1	T	C	6: 8,083,763 (GRCm39)	R565G	possibly damaging	Het
Cpvl	T	A	6: 53,944,797 (GRCm39)	I80F	probably benign	Het
Csgalnact1	T	C	8: 68,811,081 (GRCm39)	T530A	probably benign	Het
Cybrd1	A	G	2: 70,968,922 (GRCm39)	D265G	probably benign	Het
Cyp2c69	A	T	19: 39,865,986 (GRCm39)	N202K	probably benign	Het
D1Pas1	A	G	1: 186,700,205 (GRCm39)	N45D	probably damaging	Het
Dclre1a	A	G	19: 56,528,638 (GRCm39)	V839A	probably damaging	Het
Degs1	A	T	1: 182,106,630 (GRCm39)	Y210N	probably damaging	Het
Doc2g	A	G	19: 4,054,778 (GRCm39)	S220G	probably benign	Het
Epb41l2	T	A	10: 25,388,875 (GRCm39)	L885Q	probably damaging	Het
Fabp1	A	T	6: 71,180,069 (GRCm39)		probably null	Het
Fat2	G	A	11: 55,201,328 (GRCm39)	S582L	probably benign	Het
Fcgbpl1	T	A	7: 27,839,463 (GRCm39)	C425*	probably null	Het
Fras1	A	G	5: 96,857,943 (GRCm39)	N2079S	probably benign	Het
Gdf6	T	C	4: 9,860,210 (GRCm39)	Y431H	probably damaging	Het
Gm45861	T	G	8: 28,071,034 (GRCm39)	S1305A	unknown	Het
Gse1	T	C	8: 120,957,387 (GRCm39)		probably benign	Het
Kmt2e	A	G	5: 23,705,485 (GRCm39)	H1303R	possibly damaging	Het
Lck	T	C	4: 129,442,658 (GRCm39)	D499G	possibly damaging	Het
Lepr	A	T	4: 101,646,484 (GRCm39)	Y805F	probably damaging	Het
Lin7a	A	T	10: 107,218,489 (GRCm39)	Y11F	possibly damaging	Het
Lrrc43	A	G	5: 123,641,826 (GRCm39)	K559E	probably damaging	Het
Megf6	T	C	4: 154,338,602 (GRCm39)	L467P	possibly damaging	Het
Mprip	G	A	11: 59,628,215 (GRCm39)	G221R	probably damaging	Het
Myo5c	T	C	9: 75,208,738 (GRCm39)	V1683A	probably damaging	Het
Nbeal2	G	A	9: 110,467,686 (GRCm39)	R501W	probably damaging	Het
Ncf1	G	T	5: 134,254,116 (GRCm39)	A219E	possibly damaging	Het
Nckap1l	T	C	15: 103,384,493 (GRCm39)	I616T	probably benign	Het
Nlrp2	A	T	7: 5,331,228 (GRCm39)	C389*	probably null	Het
Nrg3	T	C	14: 38,098,333 (GRCm39)	E507G	probably damaging	Het
Or4p19	A	G	2: 88,242,759 (GRCm39)	L81P	probably damaging	Het
P4ha2	A	T	11: 54,022,072 (GRCm39)	T532S	probably benign	Het
Pappa	A	T	4: 65,269,955 (GRCm39)	H1623L	probably benign	Het
Paqr6	A	G	3: 88,273,353 (GRCm39)	Y115C	probably damaging	Het
Pcolce2	A	T	9: 95,560,521 (GRCm39)	Q190L	probably benign	Het
Poll	A	G	19: 45,547,277 (GRCm39)	I65T	probably benign	Het
Prmt9	T	C	8: 78,276,086 (GRCm39)		probably benign	Het
Prpf39	T	C	12: 65,100,074 (GRCm39)	V130A	possibly damaging	Het
Prpf6	A	G	2: 181,262,433 (GRCm39)	D144G	probably damaging	Het
Rgs6	T	A	12: 83,138,878 (GRCm39)		probably benign	Het
Rimbp2	A	G	5: 128,879,847 (GRCm39)		probably null	Het
Ripor2	A	G	13: 24,855,829 (GRCm39)	T90A	probably benign	Het
Rnf150	T	C	8: 83,590,706 (GRCm39)	F23S	probably damaging	Het
Rpp40	G	A	13: 36,082,889 (GRCm39)	R200W	possibly damaging	Het
Rtp3	G	A	9: 110,815,714 (GRCm39)	S217L	probably benign	Het
Sacs	A	C	14: 61,446,264 (GRCm39)	K2770T	probably benign	Het
Scn10a	A	T	9: 119,442,610 (GRCm39)	I1545N	probably damaging	Het
Scn2b	G	T	9: 45,037,438 (GRCm39)	V162L	probably damaging	Het
Sema6d	A	G	2: 124,506,831 (GRCm39)	T880A	probably damaging	Het
Slc36a4	A	G	9: 15,630,929 (GRCm39)	D16G	probably benign	Het
Slc4a8	T	A	15: 100,689,524 (GRCm39)	I378K	probably benign	Het
Smco2	T	A	6: 146,760,354 (GRCm39)	L70*	probably null	Het
Sptb	C	T	12: 76,671,862 (GRCm39)	V364I	probably damaging	Het
Susd4	A	G	1: 182,592,613 (GRCm39)	H3R	probably damaging	Het
Tbc1d16	T	C	11: 119,049,617 (GRCm39)	Q293R	probably damaging	Het
Tnfsf9	T	A	17: 57,414,317 (GRCm39)	M248K	possibly damaging	Het
Toporsl	A	G	4: 52,611,211 (GRCm39)	N368S	possibly damaging	Het
Trip11	T	C	12: 101,852,126 (GRCm39)	E361G	probably benign	Het
Trrap	T	A	5: 144,728,964 (GRCm39)	M626K	possibly damaging	Het
Ttn	A	T	2: 76,773,218 (GRCm39)	S2395T	probably damaging	Het
Ubqln3	T	C	7: 103,790,630 (GRCm39)	R487G	probably damaging	Het
Vdac1	A	G	11: 52,265,193 (GRCm39)	Y22C	probably damaging	Het
Vmn1r59	C	T	7: 5,457,477 (GRCm39)	M94I	probably benign	Het
Vmn2r10	G	T	5: 109,149,894 (GRCm39)	D383E	probably damaging	Het
Vmn2r115	T	C	17: 23,578,785 (GRCm39)	Y753H	probably damaging	Het
Vmn2r97	G	T	17: 19,134,663 (GRCm39)	C27F	probably damaging	Het
Wasf1	T	A	10: 40,812,471 (GRCm39)	V420E	unknown	Het
Zfp94	A	T	7: 24,002,821 (GRCm39)	L201Q	probably damaging	Het
Zgpat	TGGAGGAGGAGGAGGAGGA	TGGAGGAGGAGGAGGA	2: 181,007,811 (GRCm39)		probably benign	Het
Zmym4	C	A	4: 126,762,593 (GRCm39)	R1410L	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
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
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'- CAATCCCAGAGATTCTTGAACCTC -3'
(R):5'- ACTGAACCCCTAAAAGCGGG -3'

Sequencing Primer
(F):5'- AGAGATTCTTGAACCTCTTCACC -3'
(R):5'- TCGGAGCTGAGTCCCTG -3'

Posted On

2019-05-13