Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL00964:Pdgfra'

27497

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 #

IGL00964

Quality Score

Status

Chromosome

Chromosomal Location

75312953-75358876 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 75335726 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 453 (I453T)

Ref Sequence

ENSEMBL: ENSMUSP00000144543 (fasta)

Gene Model

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

AlphaFold

P26618

Predicted Effect

probably damaging
Transcript: ENSMUST00000000476
AA Change: I453T

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000000476
Gene: ENSMUSG00000029231
AA Change: I453T

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: I453T

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000127173
Gene: ENSMUSG00000029231
AA Change: I453T

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: I453T

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000143891
Gene: ENSMUSG00000029231
AA Change: I453T

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 damaging
Transcript: ENSMUST00000202186
AA Change: I453T

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

SMART Domains

Protein: ENSMUSP00000144543
Gene: ENSMUSG00000029231
AA Change: I453T

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: I453T

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000143906
Gene: ENSMUSG00000029231
AA Change: I453T

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: 38 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700008O03Rik	T	A	7: 44,009,610 (GRCm39)	*197C	probably null	Het
Acsl6	A	G	11: 54,216,472 (GRCm39)	Y213C	probably damaging	Het
Agt	T	C	8: 125,284,634 (GRCm39)		probably benign	Het
Aifm3	A	G	16: 17,318,228 (GRCm39)	D144G	probably damaging	Het
Alad	T	C	4: 62,432,330 (GRCm39)	I32V	probably benign	Het
Astn2	T	A	4: 66,103,424 (GRCm39)	M330L	unknown	Het
AU040320	T	A	4: 126,748,199 (GRCm39)	C1029*	probably null	Het
Brca2	T	A	5: 150,455,775 (GRCm39)	I172N	probably damaging	Het
Brme1	T	C	8: 84,893,343 (GRCm39)	I170T	probably benign	Het
Cdk5rap3	A	G	11: 96,800,765 (GRCm39)		probably null	Het
Dusp26	G	T	8: 31,584,136 (GRCm39)	R81L	probably benign	Het
Dync2h1	T	C	9: 7,174,881 (GRCm39)		probably benign	Het
Ehd4	A	G	2: 119,958,163 (GRCm39)	C141R	probably benign	Het
Ftsj3	G	T	11: 106,143,941 (GRCm39)	A261D	probably benign	Het
Gm5431	G	A	11: 48,780,094 (GRCm39)	T554I	probably damaging	Het
Hyls1	A	G	9: 35,473,408 (GRCm39)		probably benign	Het
Ifi213	T	A	1: 173,421,518 (GRCm39)	T124S	possibly damaging	Het
Ints10	T	A	8: 69,264,638 (GRCm39)	I457N	probably damaging	Het
Klk1b1	T	G	7: 43,620,593 (GRCm39)	S228A	possibly damaging	Het
Lpar2	T	C	8: 70,279,162 (GRCm39)	S319P	probably benign	Het
Lsr	T	C	7: 30,671,421 (GRCm39)	N104S	probably damaging	Het
Mybpc1	T	A	10: 88,391,604 (GRCm39)		probably null	Het
Nalcn	T	A	14: 123,532,796 (GRCm39)		probably benign	Het
Ovol2	G	A	2: 144,147,599 (GRCm39)	A217V	probably damaging	Het
Pcdh12	T	A	18: 38,415,784 (GRCm39)	Q447L	probably benign	Het
Ptprd	C	T	4: 75,916,793 (GRCm39)	W1037*	probably null	Het
Rabgef1	T	C	5: 130,219,863 (GRCm39)	S109P	probably damaging	Het
Rev3l	T	C	10: 39,740,802 (GRCm39)	I2995T	probably benign	Het
Slamf6	T	A	1: 171,745,347 (GRCm39)	C25S	probably null	Het
Slc28a2b	A	T	2: 122,347,527 (GRCm39)	Q229H	probably damaging	Het
Sorbs2	A	C	8: 46,248,714 (GRCm39)	N520T	probably damaging	Het
Spr-ps1	C	A	6: 85,132,016 (GRCm39)		noncoding transcript	Het
Stx4a	A	G	7: 127,441,898 (GRCm39)	Q92R	probably benign	Het
Tab2	A	C	10: 7,785,837 (GRCm39)	V638G	probably benign	Het
Trim41	C	A	11: 48,703,190 (GRCm39)	R79S	possibly damaging	Het
Ttll5	A	G	12: 85,896,057 (GRCm39)	Y135C	possibly damaging	Het
Zan	T	C	5: 137,404,203 (GRCm39)		probably benign	Het
Zdhhc14	T	A	17: 5,762,756 (GRCm39)	L220Q	probably damaging	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
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