Mutagenetix > Incidental Mutation

Incidental Mutation 'R3692:Pdgfra'

268811

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

040687-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R3692 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

75312953-75358876 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 75349948 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Phenylalanine at position 944 (Y944F)

Ref Sequence

ENSEMBL: ENSMUSP00000127173 (fasta)

Gene Model

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

AlphaFold

P26618

Predicted Effect

possibly damaging
Transcript: ENSMUST00000000476
AA Change: Y944F

PolyPhen 2 Score 0.543 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000000476
Gene: ENSMUSG00000029231
AA Change: Y944F

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

possibly damaging
Transcript: ENSMUST00000168162
AA Change: Y944F

PolyPhen 2 Score 0.543 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000127173
Gene: ENSMUSG00000029231
AA Change: Y944F

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

0.0878

Coding Region Coverage

1x: 99.1%
3x: 98.6%
10x: 97.3%
20x: 95.3%

Validation Efficiency

98% (42/43)

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: 39 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam1a	T	C	5: 121,657,385 (GRCm39)	D636G	probably damaging	Het
Adgrv1	A	G	13: 81,672,719 (GRCm39)	V2218A	possibly damaging	Het
Ano5	T	A	7: 51,240,327 (GRCm39)	Y752N	probably damaging	Het
Bltp2	A	G	11: 78,160,335 (GRCm39)	D598G	probably damaging	Het
Calca	T	C	7: 114,233,796 (GRCm39)	E45G	probably damaging	Het
Cdk8	C	T	5: 146,220,478 (GRCm39)	R166*	probably null	Het
Chsy1	T	A	7: 65,821,001 (GRCm39)	M412K	probably damaging	Het
Cic	T	A	7: 24,988,338 (GRCm39)	Y1675*	probably null	Het
Col1a2	T	A	6: 4,510,710 (GRCm39)	D53E	possibly damaging	Het
Dennd6b	A	G	15: 89,071,030 (GRCm39)		probably benign	Het
Fut10	T	A	8: 31,726,048 (GRCm39)	Y268N	possibly damaging	Het
Glrx3	T	C	7: 137,060,846 (GRCm39)		probably benign	Het
Gucy1b2	T	A	14: 62,642,076 (GRCm39)	N697I	probably damaging	Het
Ifi208	T	C	1: 173,510,438 (GRCm39)	S198P	possibly damaging	Het
Krt34	A	G	11: 99,929,857 (GRCm39)	V213A	probably damaging	Het
Lats2	T	C	14: 57,928,998 (GRCm39)	N959S	probably damaging	Het
Mat1a	A	G	14: 40,843,338 (GRCm39)	Y288C	probably damaging	Het
Mtif2	A	T	11: 29,490,718 (GRCm39)	H474L	probably benign	Het
Myh8	A	G	11: 67,192,744 (GRCm39)	I1512V	probably damaging	Het
Nkx2-6	T	C	14: 69,409,476 (GRCm39)	S76P	probably benign	Het
Noxred1	G	A	12: 87,280,240 (GRCm39)	R31W	probably benign	Het
Or14c46	T	A	7: 85,918,703 (GRCm39)	Q98L	probably damaging	Het
Or4a69	T	A	2: 89,313,240 (GRCm39)	M80L	probably benign	Het
Pcdhb16	C	A	18: 37,611,340 (GRCm39)	T100K	probably benign	Het
Pcdhga10	T	C	18: 37,881,384 (GRCm39)	C382R	probably damaging	Het
Pkhd1	A	G	1: 20,625,353 (GRCm39)	I741T	possibly damaging	Het
Ppp1r10	A	G	17: 36,241,760 (GRCm39)	D845G	unknown	Het
Rfk	C	A	19: 17,376,834 (GRCm39)		probably null	Het
Rgs11	C	T	17: 26,423,302 (GRCm39)		probably benign	Het
Spata31d1b	T	C	13: 59,865,705 (GRCm39)	V951A	probably benign	Het
St3gal5	T	C	6: 72,126,013 (GRCm39)	V286A	probably benign	Het
St7l	T	C	3: 104,798,870 (GRCm39)	M320T	probably benign	Het
Tnfrsf1b	G	T	4: 144,954,092 (GRCm39)	Q86K	probably benign	Het
Tox	T	C	4: 6,697,535 (GRCm39)	I423V	probably benign	Het
Tpbpa	T	A	13: 61,087,827 (GRCm39)	H88L	probably benign	Het
Vmn1r236	A	G	17: 21,507,068 (GRCm39)	Y62C	probably benign	Het
Ythdc1	A	G	5: 86,970,526 (GRCm39)	I399M	probably damaging	Het
Zfp948	T	G	17: 21,807,838 (GRCm39)	D343E	probably benign	Het
Zswim6	A	G	13: 107,863,076 (GRCm39)		noncoding transcript	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
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
R4795:Pdgfra	UTSW	5	75,349,972 (GRCm39)	missense	probably benign
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'- GATGGCCAAACCTGACCATG -3'
(R):5'- AAAGCCCTGGTCACAAGATC -3'

Sequencing Primer
(F):5'- CATGCCACCAGTGAAGTGTG -3'
(R):5'- TGGTCACAAGATCACACAATCCG -3'

Posted On

2015-02-19