Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL01556:Pdgfra'

90730

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Pdgfra

Ensembl Gene

ENSMUSG00000029231

Gene Name

platelet derived growth factor receptor, alpha polypeptide

Synonyms

Pdgfr-2, CD140a

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

IGL01556

Quality Score

Status

Chromosome

Chromosomal Location

75312953-75358876 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 75338352 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Phenylalanine at position 535 (L535F)

Ref Sequence

ENSEMBL: ENSMUSP00000143906 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000000476] [ENSMUST00000168162] [ENSMUST00000201711] [ENSMUST00000202186] [ENSMUST00000202681]

AlphaFold

P26618

Predicted Effect

probably damaging
Transcript: ENSMUST00000000476
AA Change: L535F

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

SMART Domains

Protein: ENSMUSP00000000476
Gene: ENSMUSG00000029231
AA Change: L535F

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 damaging
Transcript: ENSMUST00000168162
AA Change: L535F

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

SMART Domains

Protein: ENSMUSP00000127173
Gene: ENSMUSG00000029231
AA Change: L535F

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

noncoding transcript
Transcript: ENSMUST00000183797

Predicted Effect

probably damaging
Transcript: ENSMUST00000201711
AA Change: L535F

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

SMART Domains

Protein: ENSMUSP00000143891
Gene: ENSMUSG00000029231
AA Change: L535F

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
Pfam:Pkinase	593	701	9.9e-14	PFAM
Pfam:Pkinase_Tyr	593	750	5.2e-32	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000202186

SMART Domains

Protein: ENSMUSP00000144543
Gene: ENSMUSG00000029231

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
IG	34	122	2.6e-5	SMART
IG_like	135	206	7e-2	SMART
IGc2	226	297	3.6e-6	SMART
IG	322	414	1.2e-2	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000202681
AA Change: L535F

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

SMART Domains

Protein: ENSMUSP00000143906
Gene: ENSMUSG00000029231
AA Change: L535F

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
Pfam:Pkinase	593	701	9.9e-14	PFAM
Pfam:Pkinase_Tyr	593	750	5.2e-32	PFAM

Coding Region Coverage

Validation Efficiency

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: 34 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamts18	T	C	8: 114,571,741 (GRCm39)	I81V	probably benign	Het
Aoc1l1	A	C	6: 48,952,618 (GRCm39)	D181A	possibly damaging	Het
Armc3	T	A	2: 19,273,957 (GRCm39)	D330E	probably damaging	Het
Atp6v0b	A	G	4: 117,743,062 (GRCm39)	F49S	probably damaging	Het
Atp8b3	A	C	10: 80,366,802 (GRCm39)	Y265*	probably null	Het
Cby2	A	G	14: 75,821,551 (GRCm39)	F16S	probably damaging	Het
Cdh11	A	G	8: 103,406,276 (GRCm39)	Y66H	probably damaging	Het
Cntn5	T	A	9: 9,673,913 (GRCm39)	M730L	probably benign	Het
Cntrl	A	G	2: 35,063,071 (GRCm39)	T1556A	probably benign	Het
Dixdc1	A	G	9: 50,617,434 (GRCm39)	S128P	probably damaging	Het
Egfr	T	C	11: 16,855,382 (GRCm39)	L889S	probably damaging	Het
F830045P16Rik	A	G	2: 129,305,640 (GRCm39)	Y245H	probably benign	Het
Fam124a	G	A	14: 62,825,181 (GRCm39)	C225Y	probably damaging	Het
Frem2	T	C	3: 53,442,702 (GRCm39)	T2612A	probably benign	Het
Gkap1	A	T	13: 58,411,106 (GRCm39)	I89N	probably benign	Het
Gm8247	A	T	14: 44,823,811 (GRCm39)	K75*	probably null	Het
Gpi-ps	A	G	8: 5,689,833 (GRCm39)		noncoding transcript	Het
Hdac11	T	A	6: 91,150,162 (GRCm39)	H320Q	probably benign	Het
Iyd	A	G	10: 3,497,091 (GRCm39)	I149V	probably benign	Het
Krtap4-6	T	A	11: 99,556,676 (GRCm39)	Q17L	unknown	Het
Lrrc24	T	A	15: 76,606,775 (GRCm39)	D207V	probably damaging	Het
Mfsd12	G	A	10: 81,198,858 (GRCm39)	C425Y	probably damaging	Het
Muc5b	A	G	7: 141,416,977 (GRCm39)	T3308A	probably benign	Het
Myo18b	A	G	5: 112,905,315 (GRCm39)		probably benign	Het
Ndufa6	C	T	15: 82,238,282 (GRCm39)	V50M	possibly damaging	Het
Nin	A	G	12: 70,089,962 (GRCm39)	V1151A	probably benign	Het
Nrf1	A	G	6: 30,126,366 (GRCm39)		probably benign	Het
Pcdhb20	T	C	18: 37,637,852 (GRCm39)	I126T	possibly damaging	Het
Pkn2	A	T	3: 142,535,078 (GRCm39)	I212K	possibly damaging	Het
Slc5a9	T	A	4: 111,755,833 (GRCm39)	T22S	probably benign	Het
Slitrk1	A	G	14: 109,150,450 (GRCm39)	L87S	probably damaging	Het
Syne2	C	A	12: 76,134,589 (GRCm39)	R29S	probably damaging	Het
Zc3h12b	C	A	X: 94,970,721 (GRCm39)	F551L	probably damaging	Het
Zfp664	C	A	5: 124,963,252 (GRCm39)	C215*	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
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
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

Posted On

2013-12-09