Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL00906:Pdgfra'

27387

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 #

IGL00906

Quality Score

Status

Chromosome

Chromosomal Location

75312953-75358876 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 75340834 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Valine at position 598 (I598V)

Ref Sequence

ENSEMBL: ENSMUSP00000143906 (fasta)

Gene Model

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

AlphaFold

P26618

Predicted Effect

probably benign
Transcript: ENSMUST00000000476
AA Change: I598V

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000000476
Gene: ENSMUSG00000029231
AA Change: I598V

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: I598V

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000127173
Gene: ENSMUSG00000029231
AA Change: I598V

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 benign
Transcript: ENSMUST00000201711
AA Change: I598V

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000143891
Gene: ENSMUSG00000029231
AA Change: I598V

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: ENSMUST00000202681
AA Change: I598V

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000143906
Gene: ENSMUSG00000029231
AA Change: I598V

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: 36 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aacs	A	G	5: 125,580,338 (GRCm39)	E221G	probably benign	Het
Alb	A	G	5: 90,619,932 (GRCm39)	N453S	probably benign	Het
Bckdha	C	T	7: 25,332,767 (GRCm39)	V183M	probably benign	Het
Brpf3	A	G	17: 29,055,674 (GRCm39)		probably benign	Het
Ccdc163	T	C	4: 116,567,487 (GRCm39)		probably null	Het
Ccdc178	A	T	18: 22,268,225 (GRCm39)	C87*	probably null	Het
Cfhr4	A	T	1: 139,659,312 (GRCm39)	V739E	probably damaging	Het
Clca4a	A	G	3: 144,660,700 (GRCm39)	V708A	probably damaging	Het
Cyfip2	A	G	11: 46,091,512 (GRCm39)	V1136A	possibly damaging	Het
Dnah11	A	C	12: 117,874,937 (GRCm39)	L3976R	probably damaging	Het
Erich1	A	G	8: 14,083,770 (GRCm39)		probably benign	Het
Fam228a	A	T	12: 4,782,773 (GRCm39)	Y107N	possibly damaging	Het
Iars2	A	T	1: 185,028,600 (GRCm39)		probably benign	Het
Ifi204	A	G	1: 173,587,197 (GRCm39)		probably benign	Het
Ifih1	A	T	2: 62,476,168 (GRCm39)	I36N	probably benign	Het
Jak1	C	T	4: 101,011,826 (GRCm39)	G1092D	probably damaging	Het
Kir3dl2	G	A	X: 135,357,097 (GRCm39)	P122S	probably damaging	Het
Nacc2	T	C	2: 25,951,678 (GRCm39)	T386A	probably damaging	Het
Nrf1	C	T	6: 30,098,477 (GRCm39)	T135M	probably damaging	Het
Or4k15	A	G	14: 50,364,214 (GRCm39)	Y60C	probably damaging	Het
Or51i2	G	A	7: 103,689,051 (GRCm39)	G16D	probably damaging	Het
Pcca	A	C	14: 122,927,545 (GRCm39)	D436A	probably benign	Het
Pcdhb11	A	T	18: 37,555,174 (GRCm39)	Q168L	possibly damaging	Het
Pla2g6	C	T	15: 79,171,947 (GRCm39)	V637I	probably damaging	Het
Plac1	A	C	X: 52,159,593 (GRCm39)	V39G	probably damaging	Het
Pparg	A	G	6: 115,416,822 (GRCm39)	E5G	probably damaging	Het
Ppp1r9a	A	G	6: 5,157,023 (GRCm39)	D967G	possibly damaging	Het
Rel	T	C	11: 23,694,266 (GRCm39)	T322A	probably benign	Het
Sgk3	A	G	1: 9,947,470 (GRCm39)	T137A	probably benign	Het
Sgpp2	A	G	1: 78,367,184 (GRCm39)	R106G	probably benign	Het
Slc27a5	T	A	7: 12,724,984 (GRCm39)	M459L	probably benign	Het
Snx21	T	C	2: 164,628,140 (GRCm39)	L52P	probably damaging	Het
Srarp	G	A	4: 141,160,584 (GRCm39)	T83M	probably benign	Het
Sstr2	A	G	11: 113,515,821 (GRCm39)	R247G	probably benign	Het
Tnpo3	G	A	6: 29,589,047 (GRCm39)	S101L	probably damaging	Het
Zan	A	G	5: 137,387,622 (GRCm39)	I4863T	unknown	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
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
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

2013-04-17