Mutagenetix > Incidental Mutation

Incidental Mutation 'R4795:Pdgfra'

368923

Institutional Source

Beutler Lab

Gene Symbol

Pdgfra

Ensembl Gene

ENSMUSG00000029231

Gene Name

platelet derived growth factor receptor, alpha polypeptide

Synonyms

Pdgfr-2, CD140a

MMRRC Submission

041996-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4795 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

75312953-75358876 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 75349972 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Serine at position 952 (N952S)

Ref Sequence

ENSEMBL: ENSMUSP00000127173 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000000476] [ENSMUST00000168162]

AlphaFold

P26618

Predicted Effect

probably benign
Transcript: ENSMUST00000000476
AA Change: N952S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000000476
Gene: ENSMUSG00000029231
AA Change: N952S

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
IG	34	122	6.07e-3	SMART
IG_like	135	206	1.7e1	SMART
IGc2	226	297	8.72e-4	SMART
IG	322	414	2.86e0	SMART
transmembrane domain	527	549	N/A	INTRINSIC
TyrKc	593	950	8.51e-141	SMART
Blast:TyrKc	960	991	3e-8	BLAST
low complexity region	1063	1082	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000168162
AA Change: N952S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000127173
Gene: ENSMUSG00000029231
AA Change: N952S

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
IG	34	122	6.07e-3	SMART
IG_like	135	206	1.7e1	SMART
IGc2	226	297	8.72e-4	SMART
IG	322	414	2.86e0	SMART
transmembrane domain	527	549	N/A	INTRINSIC
TyrKc	593	950	8.51e-141	SMART
Blast:TyrKc	960	991	3e-8	BLAST
low complexity region	1063	1082	N/A	INTRINSIC

Meta Mutation Damage Score

0.0889

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.7%
20x: 93.7%

Validation Efficiency

98% (123/125)

MGI Phenotype

FUNCTION: This gene encodes a member of the receptor tyrosine kinase family of proteins. Binding of platelet-derived growth factor protein ligands to this receptor triggers receptor dimerization and autophosphorylation, resulting in the activation of several downstream signaling pathways. Signaling through the encoded receptor plays a role in gastrulation and the development of nearly all organ systems. Mice lacking a functional copy of this gene reportedly exhibit defects in lung, skeleton, testis and the central nervous system, and die soon after birth. Alternative splicing and intronic polyadenylation of gene transcripts have been implicated in muscle regeneration and fibrosis in adult mice. [provided by RefSeq, Jan 2017]
PHENOTYPE: Homozygotes for targeted null mutations exhibit incomplete cephalic closure, increased apoptosis of neural crest cells, impaired myotome and testis formation, abnormal mucosal linings, thoracic skeletal defects, and midgestational lethality. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 105 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca4	T	G	3: 121,969,772 (GRCm39)	L2259R	probably damaging	Het
Acd	A	G	8: 106,427,647 (GRCm39)	S2P	possibly damaging	Het
Acsf3	A	G	8: 123,506,896 (GRCm39)	Y63C	possibly damaging	Het
Adam21	T	C	12: 81,607,748 (GRCm39)	I5V	probably benign	Het
Adamts6	C	A	13: 104,580,636 (GRCm39)	S783*	probably null	Het
Adamtsl1	T	C	4: 86,162,006 (GRCm39)		probably null	Het
Adck2	T	A	6: 39,553,327 (GRCm39)	S313T	probably benign	Het
Adgb	A	G	10: 10,233,616 (GRCm39)	I1285T	probably benign	Het
Angptl1	T	A	1: 156,688,153 (GRCm39)	M485K	possibly damaging	Het
Ank3	G	A	10: 69,694,095 (GRCm39)	V289I	probably benign	Het
Atp13a4	A	G	16: 29,308,826 (GRCm39)		probably null	Het
Atp1a1	A	G	3: 101,491,091 (GRCm39)	L648P	probably benign	Het
Atp2a3	A	G	11: 72,863,855 (GRCm39)	I194V	probably benign	Het
Bglap	A	C	3: 88,291,712 (GRCm39)	I4S	unknown	Het
Cacna1b	T	A	2: 24,527,499 (GRCm39)	T1621S	possibly damaging	Het
Ccdc112	T	A	18: 46,420,739 (GRCm39)	Q337L	probably benign	Het
Ccdc121rt3	A	G	5: 112,503,165 (GRCm39)	S180P	possibly damaging	Het
Cd34	T	G	1: 194,633,319 (GRCm39)	S194A	probably damaging	Het
Cdh20	A	G	1: 104,868,989 (GRCm39)	D160G	probably damaging	Het
Clock	T	C	5: 76,413,763 (GRCm39)	K44R	probably damaging	Het
Commd9	A	G	2: 101,729,241 (GRCm39)	N116D	probably benign	Het
Dab2	C	A	15: 6,459,092 (GRCm39)	P335T	probably benign	Het
Epb41l3	T	A	17: 69,555,714 (GRCm39)		probably null	Het
Epha2	A	G	4: 141,049,727 (GRCm39)		probably null	Het
Fam78b	T	C	1: 166,906,216 (GRCm39)	V125A	probably benign	Het
Fars2	A	T	13: 36,721,400 (GRCm39)	E448V	probably damaging	Het
Fkbpl	G	A	17: 34,864,303 (GRCm39)	A24T	probably benign	Het
Glyr1	A	C	16: 4,865,622 (GRCm39)	V44G	probably benign	Het
Gm1527	A	G	3: 28,974,812 (GRCm39)	I542V	possibly damaging	Het
Gm18856	C	A	13: 14,139,793 (GRCm39)		probably benign	Het
Gm44501	A	G	17: 40,889,605 (GRCm39)	K40E	probably benign	Het
Hdhd5	T	C	6: 120,500,407 (GRCm39)	H97R	probably benign	Het
Hmcn1	A	G	1: 150,629,362 (GRCm39)	V965A	probably benign	Het
Hsf5	A	G	11: 87,526,446 (GRCm39)	M373V	probably benign	Het
Igbp1b	C	T	6: 138,634,803 (GRCm39)	E214K	probably benign	Het
Iigp1	T	A	18: 60,522,964 (GRCm39)	F27L	probably benign	Het
Isl1	T	C	13: 116,441,966 (GRCm39)	N89S	probably benign	Het
Itga1	C	A	13: 115,171,921 (GRCm39)	W61C	probably damaging	Het
Itga5	T	C	15: 103,256,187 (GRCm39)	R922G	probably benign	Het
Kbtbd3	G	A	9: 4,331,073 (GRCm39)	W482*	probably null	Het
Kcnq1	A	G	7: 142,736,494 (GRCm39)	T168A	probably benign	Het
Lrch3	A	G	16: 32,826,074 (GRCm39)	N631S	probably damaging	Het
Lrrk1	T	A	7: 65,912,413 (GRCm39)	I1716F	possibly damaging	Het
Ly75	T	C	2: 60,180,284 (GRCm39)	E631G	probably benign	Het
Map4	T	C	9: 109,864,331 (GRCm39)	S519P	probably benign	Het
Mroh2a	A	G	1: 88,186,386 (GRCm39)	S64G	probably benign	Het
Mrtfa	C	T	15: 80,901,234 (GRCm39)	S419N	probably damaging	Het
Muc5b	A	G	7: 141,403,304 (GRCm39)	E755G	unknown	Het
Ncaph2	T	G	15: 89,255,010 (GRCm39)	V478G	probably damaging	Het
Ncbp1	A	G	4: 46,152,967 (GRCm39)	R247G	possibly damaging	Het
Necab1	G	T	4: 15,111,208 (GRCm39)	D73E	possibly damaging	Het
Nedd9	T	C	13: 41,471,376 (GRCm39)	K208E	probably benign	Het
Nfyb	A	T	10: 82,588,202 (GRCm39)		probably benign	Het
Nol4	T	C	18: 23,054,944 (GRCm39)	Q162R	probably damaging	Het
Nwd2	G	A	5: 63,962,776 (GRCm39)	D787N	probably benign	Het
Olfr908	T	A	9: 38,427,799 (GRCm39)	M157K	probably damaging	Het
Or10a5	A	T	7: 106,636,121 (GRCm39)	Y253F	probably benign	Het
Or11g7	A	C	14: 50,690,874 (GRCm39)	M122L	probably damaging	Het
Or13a22	A	G	7: 140,072,920 (GRCm39)	D123G	probably damaging	Het
Or5ac23	C	T	16: 59,149,213 (GRCm39)	V220I	probably benign	Het
Or6a2	C	T	7: 106,600,542 (GRCm39)	G175D	probably damaging	Het
Or6e1	A	G	14: 54,520,004 (GRCm39)	M116T	probably damaging	Het
Orai3	T	C	7: 127,373,060 (GRCm39)	V187A	probably benign	Het
Parn	T	C	16: 13,424,066 (GRCm39)	T444A	probably benign	Het
Pcdh11x	A	C	X: 119,309,937 (GRCm39)	N460T	probably damaging	Het
Pcnt	C	T	10: 76,205,858 (GRCm39)	R2516H	probably benign	Het
Pde4d	T	A	13: 110,074,705 (GRCm39)		probably benign	Het
Pgm2	A	G	5: 64,261,217 (GRCm39)	Y237C	probably damaging	Het
Plcb2	A	G	2: 118,541,605 (GRCm39)	V975A	probably benign	Het
Polk	T	C	13: 96,625,764 (GRCm39)	T347A	probably benign	Het
Ppp6r1	C	T	7: 4,644,053 (GRCm39)	V430M	possibly damaging	Het
Ptges2	C	A	2: 32,286,334 (GRCm39)	C16*	probably null	Het
Relb	A	T	7: 19,353,764 (GRCm39)	I38N	probably damaging	Het
Runx1t1	T	A	4: 13,837,767 (GRCm39)	N51K	probably damaging	Het
Samsn1	A	G	16: 75,680,733 (GRCm39)		probably benign	Het
Scrn1	A	G	6: 54,497,754 (GRCm39)	V279A	possibly damaging	Het
Sec31b	A	G	19: 44,520,185 (GRCm39)	S200P	probably benign	Het
Selp	A	G	1: 163,972,475 (GRCm39)	T705A	probably benign	Het
Slc2a1	G	A	4: 118,989,642 (GRCm39)	R61Q	probably damaging	Het
Slit3	G	A	11: 35,542,647 (GRCm39)		probably null	Het
Smo	T	A	6: 29,755,573 (GRCm39)	V415E	probably damaging	Het
Spag8	C	A	4: 43,652,035 (GRCm39)	V350L	possibly damaging	Het
Tbck	T	G	3: 132,413,559 (GRCm39)	L132R	possibly damaging	Het
Thnsl1	T	A	2: 21,216,856 (GRCm39)	C203*	probably null	Het
Tm9sf2	T	A	14: 122,387,252 (GRCm39)		probably null	Het
Tmem131	A	G	1: 36,880,757 (GRCm39)	V171A	probably damaging	Het
Tmem209	T	C	6: 30,501,954 (GRCm39)	T83A	probably benign	Het
Tmem63a	T	C	1: 180,782,416 (GRCm39)	Y138H	probably damaging	Het
Trim80	A	G	11: 115,338,769 (GRCm39)	Y533C	probably damaging	Het
Trpv2	A	G	11: 62,472,006 (GRCm39)	D66G	possibly damaging	Het
Trrap	T	A	5: 144,769,298 (GRCm39)	I2620N	probably benign	Het
Ttyh3	A	T	5: 140,620,541 (GRCm39)	I232N	probably damaging	Het
Ube2dnl1	G	A	X: 113,815,482 (GRCm39)	C119Y	possibly damaging	Het
Unc13c	T	A	9: 73,839,469 (GRCm39)	S461C	probably damaging	Het
Unc80	T	G	1: 66,567,100 (GRCm39)	I902S	probably damaging	Het
Usp42	C	A	5: 143,709,692 (GRCm39)	G170W	probably damaging	Het
Vldlr	T	C	19: 27,216,252 (GRCm39)		probably null	Het
Ywhab	A	G	2: 163,857,265 (GRCm39)	Y180C	probably damaging	Het
Zan	A	T	5: 137,379,112 (GRCm39)	C5329*	probably null	Het
Zbtb40	C	T	4: 136,725,953 (GRCm39)	M535I	probably benign	Het
Zdhhc1	CGGGGG	CGGGGGG	8: 106,210,376 (GRCm39)		probably null	Het
Zfp318	A	G	17: 46,722,988 (GRCm39)	T1664A	probably benign	Het
Zfp7	T	A	15: 76,775,546 (GRCm39)	C529*	probably null	Het
Zfp768	T	C	7: 126,942,547 (GRCm39)	Q527R	possibly damaging	Het
Zfp975	T	A	7: 42,314,570 (GRCm39)		probably null	Het

Other mutations in Pdgfra

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00489:Pdgfra	APN	5	75,324,340 (GRCm39)	missense	probably benign	0.40
IGL00574:Pdgfra	APN	5	75,341,708 (GRCm39)	missense	probably damaging	1.00
IGL00906:Pdgfra	APN	5	75,340,834 (GRCm39)	missense	probably benign	0.00
IGL00964:Pdgfra	APN	5	75,335,726 (GRCm39)	missense	probably damaging	1.00
IGL01467:Pdgfra	APN	5	75,346,292 (GRCm39)	critical splice donor site	probably null
IGL01485:Pdgfra	APN	5	75,324,313 (GRCm39)	missense	probably benign	0.02
IGL01556:Pdgfra	APN	5	75,338,352 (GRCm39)	missense	probably damaging	1.00
IGL01949:Pdgfra	APN	5	75,331,326 (GRCm39)	missense	probably damaging	0.98
IGL02066:Pdgfra	APN	5	75,331,241 (GRCm39)	missense	possibly damaging	0.55
IGL02271:Pdgfra	APN	5	75,348,567 (GRCm39)	missense	probably damaging	1.00
IGL02726:Pdgfra	APN	5	75,355,618 (GRCm39)	nonsense	probably null
IGL02858:Pdgfra	APN	5	75,355,635 (GRCm39)	missense	probably damaging	1.00
IGL03306:Pdgfra	APN	5	75,353,194 (GRCm39)	missense	possibly damaging	0.49
Pony_express	UTSW	5	75,349,895 (GRCm39)	nonsense	probably null
P0033:Pdgfra	UTSW	5	75,353,222 (GRCm39)	missense	probably damaging	1.00
PIT4472001:Pdgfra	UTSW	5	75,340,907 (GRCm39)	missense	probably damaging	1.00
R0134:Pdgfra	UTSW	5	75,327,172 (GRCm39)	missense	probably damaging	1.00
R0200:Pdgfra	UTSW	5	75,324,438 (GRCm39)	missense	probably damaging	1.00
R0254:Pdgfra	UTSW	5	75,328,596 (GRCm39)	missense	probably damaging	1.00
R0331:Pdgfra	UTSW	5	75,355,713 (GRCm39)	missense	probably damaging	1.00
R0467:Pdgfra	UTSW	5	75,355,697 (GRCm39)	missense	probably damaging	1.00
R0532:Pdgfra	UTSW	5	75,331,434 (GRCm39)	missense	probably benign	0.00
R0608:Pdgfra	UTSW	5	75,324,438 (GRCm39)	missense	probably damaging	1.00
R0765:Pdgfra	UTSW	5	75,348,648 (GRCm39)	unclassified	probably benign
R1171:Pdgfra	UTSW	5	75,334,108 (GRCm39)	missense	probably damaging	0.98
R1372:Pdgfra	UTSW	5	75,349,924 (GRCm39)	missense	probably damaging	0.96
R1530:Pdgfra	UTSW	5	75,349,671 (GRCm39)	splice site	probably null
R1585:Pdgfra	UTSW	5	75,353,264 (GRCm39)	missense	probably damaging	1.00
R1666:Pdgfra	UTSW	5	75,349,681 (GRCm39)	missense	possibly damaging	0.94
R1836:Pdgfra	UTSW	5	75,343,675 (GRCm39)	missense	possibly damaging	0.95
R1868:Pdgfra	UTSW	5	75,331,534 (GRCm39)	missense	probably benign	0.43
R1923:Pdgfra	UTSW	5	75,324,394 (GRCm39)	missense	probably benign	0.03
R2075:Pdgfra	UTSW	5	75,348,609 (GRCm39)	missense	probably damaging	1.00
R2261:Pdgfra	UTSW	5	75,346,184 (GRCm39)	missense	probably benign	0.03
R2262:Pdgfra	UTSW	5	75,346,184 (GRCm39)	missense	probably benign	0.03
R3028:Pdgfra	UTSW	5	75,335,642 (GRCm39)	missense	probably damaging	1.00
R3236:Pdgfra	UTSW	5	75,328,597 (GRCm39)	missense	probably damaging	1.00
R3692:Pdgfra	UTSW	5	75,349,948 (GRCm39)	missense	possibly damaging	0.54
R3701:Pdgfra	UTSW	5	75,340,881 (GRCm39)	nonsense	probably null
R3890:Pdgfra	UTSW	5	75,328,588 (GRCm39)	missense	probably null	0.57
R3901:Pdgfra	UTSW	5	75,353,169 (GRCm39)	missense	probably benign	0.10
R3902:Pdgfra	UTSW	5	75,353,169 (GRCm39)	missense	probably benign	0.10
R4272:Pdgfra	UTSW	5	75,343,731 (GRCm39)	missense	probably benign	0.05
R4532:Pdgfra	UTSW	5	75,341,744 (GRCm39)	missense	probably damaging	1.00
R4660:Pdgfra	UTSW	5	75,322,932 (GRCm39)	missense	possibly damaging	0.82
R4753:Pdgfra	UTSW	5	75,342,185 (GRCm39)	missense	probably damaging	1.00
R4796:Pdgfra	UTSW	5	75,349,972 (GRCm39)	missense	probably benign
R4884:Pdgfra	UTSW	5	75,349,973 (GRCm39)	missense	probably benign	0.07
R4936:Pdgfra	UTSW	5	75,355,687 (GRCm39)	missense	probably damaging	1.00
R5625:Pdgfra	UTSW	5	75,349,998 (GRCm39)	critical splice donor site	probably null
R5666:Pdgfra	UTSW	5	75,334,156 (GRCm39)	missense	probably benign	0.00
R5670:Pdgfra	UTSW	5	75,334,156 (GRCm39)	missense	probably benign	0.00
R5714:Pdgfra	UTSW	5	75,346,673 (GRCm39)	missense	probably damaging	1.00
R5836:Pdgfra	UTSW	5	75,324,435 (GRCm39)	missense	possibly damaging	0.52
R6126:Pdgfra	UTSW	5	75,331,190 (GRCm39)	missense	probably benign	0.09
R6141:Pdgfra	UTSW	5	75,334,057 (GRCm39)	missense	probably damaging	0.98
R6297:Pdgfra	UTSW	5	75,334,135 (GRCm39)	missense	possibly damaging	0.88
R6363:Pdgfra	UTSW	5	75,331,497 (GRCm39)	missense	possibly damaging	0.91
R6376:Pdgfra	UTSW	5	75,327,180 (GRCm39)	missense	probably benign	0.02
R6485:Pdgfra	UTSW	5	75,335,735 (GRCm39)	splice site	probably null
R6612:Pdgfra	UTSW	5	75,328,503 (GRCm39)	missense	probably benign	0.01
R6641:Pdgfra	UTSW	5	75,322,762 (GRCm39)	intron	probably benign
R6954:Pdgfra	UTSW	5	75,334,055 (GRCm39)	missense	possibly damaging	0.82
R7110:Pdgfra	UTSW	5	75,349,895 (GRCm39)	nonsense	probably null
R7192:Pdgfra	UTSW	5	75,343,767 (GRCm39)	missense	probably damaging	1.00
R7294:Pdgfra	UTSW	5	75,342,312 (GRCm39)	missense	probably benign	0.05
R7347:Pdgfra	UTSW	5	75,343,759 (GRCm39)	missense	possibly damaging	0.91
R7476:Pdgfra	UTSW	5	75,331,264 (GRCm39)	missense	probably damaging	1.00
R7512:Pdgfra	UTSW	5	75,355,675 (GRCm39)	nonsense	probably null
R7609:Pdgfra	UTSW	5	75,327,382 (GRCm39)	missense	probably benign	0.10
R7925:Pdgfra	UTSW	5	75,353,079 (GRCm39)	splice site	probably benign
R8141:Pdgfra	UTSW	5	75,338,387 (GRCm39)	missense	possibly damaging	0.81
R8490:Pdgfra	UTSW	5	75,331,329 (GRCm39)	critical splice donor site	probably null
R8886:Pdgfra	UTSW	5	75,343,734 (GRCm39)	missense	probably benign	0.03
R9234:Pdgfra	UTSW	5	75,324,262 (GRCm39)	missense	possibly damaging	0.93
R9339:Pdgfra	UTSW	5	75,355,635 (GRCm39)	missense	probably damaging	1.00
R9459:Pdgfra	UTSW	5	75,353,129 (GRCm39)	missense	probably damaging	1.00
R9475:Pdgfra	UTSW	5	75,328,588 (GRCm39)	missense	possibly damaging	0.93
R9519:Pdgfra	UTSW	5	75,337,350 (GRCm39)	missense	probably benign	0.00
Z1088:Pdgfra	UTSW	5	75,327,238 (GRCm39)	missense	probably benign	0.03
Z1177:Pdgfra	UTSW	5	75,342,335 (GRCm39)	missense	probably null	1.00

Predicted Primers

PCR Primer
(F):5'- AGTGAAGTGTGAGCTTCCTCC -3'
(R):5'- AGTGCTACTGGGGTCCTATAG -3'

Sequencing Primer
(F):5'- GAGCTTCCTCCTCACCCACG -3'
(R):5'- GGGGTCCTATAGAGCACTCC -3'

Posted On

2016-02-04