Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL00489:Pdgfra'

5613

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 #

IGL00489

Quality Score

Status

Chromosome

Chromosomal Location

75312953-75358876 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 75324340 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 65 (D65G)

Ref Sequence

ENSEMBL: ENSMUSP00000144485 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000000476] [ENSMUST00000168162] [ENSMUST00000200822] [ENSMUST00000201711] [ENSMUST00000202161] [ENSMUST00000202186] [ENSMUST00000202681] [ENSMUST00000202992]

AlphaFold

P26618

Predicted Effect

probably benign
Transcript: ENSMUST00000000476
AA Change: D65G

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

SMART Domains

Protein: ENSMUSP00000000476
Gene: ENSMUSG00000029231
AA Change: D65G

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: D65G

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

SMART Domains

Protein: ENSMUSP00000127173
Gene: ENSMUSG00000029231
AA Change: D65G

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: ENSMUST00000200822
AA Change: D65G

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

SMART Domains

Protein: ENSMUSP00000144634
Gene: ENSMUSG00000029231
AA Change: D65G

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
Blast:IG	220	243	3e-6	BLAST

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000201241

Predicted Effect

probably benign
Transcript: ENSMUST00000201711
AA Change: D65G

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

SMART Domains

Protein: ENSMUSP00000143891
Gene: ENSMUSG00000029231
AA Change: D65G

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: ENSMUST00000202161
AA Change: D65G

PolyPhen 2 Score 0.404 (Sensitivity: 0.89; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000144485
Gene: ENSMUSG00000029231
AA Change: D65G

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
Blast:IG	34	88	5e-32	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000202186
AA Change: D65G

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

SMART Domains

Protein: ENSMUSP00000144543
Gene: ENSMUSG00000029231
AA Change: D65G

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 benign
Transcript: ENSMUST00000202681
AA Change: D65G

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

SMART Domains

Protein: ENSMUSP00000143906
Gene: ENSMUSG00000029231
AA Change: D65G

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: ENSMUST00000202992
AA Change: D65G

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

SMART Domains

Protein: ENSMUSP00000144132
Gene: ENSMUSG00000029231
AA Change: D65G

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
IG	34	122	2.6e-5	SMART

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: 29 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrg6	T	C	10: 14,316,147 (GRCm39)		probably null	Het
Alcam	T	A	16: 52,115,380 (GRCm39)		probably benign	Het
Aspm	C	A	1: 139,406,429 (GRCm39)	A1772E	probably damaging	Het
Bag6	T	A	17: 35,363,627 (GRCm39)	D770E	probably damaging	Het
Baz2b	A	T	2: 59,788,019 (GRCm39)	Y724*	probably null	Het
Ccdc178	A	T	18: 21,977,968 (GRCm39)	I833N	probably benign	Het
Ccdc28a	C	A	10: 18,106,261 (GRCm39)	V22F	possibly damaging	Het
Cmya5	T	C	13: 93,229,628 (GRCm39)	N1820S	probably benign	Het
Fancm	T	G	12: 65,152,967 (GRCm39)	I1141S	probably benign	Het
Fgfrl1	G	A	5: 108,853,753 (GRCm39)	G287S	probably damaging	Het
Galntl6	G	A	8: 58,310,574 (GRCm39)	P376S	probably damaging	Het
Gm21985	A	G	2: 112,168,342 (GRCm39)		probably benign	Het
Hck	A	G	2: 152,992,939 (GRCm39)	E482G	possibly damaging	Het
Kcna3	C	T	3: 106,944,472 (GRCm39)	S245L	probably benign	Het
Mcc	T	C	18: 44,582,283 (GRCm39)	M798V	possibly damaging	Het
Nlrp9c	T	C	7: 26,084,013 (GRCm39)	Y522C	probably benign	Het
Ofcc1	C	A	13: 40,433,967 (GRCm39)	S46I	probably damaging	Het
Phf24	A	C	4: 42,933,905 (GRCm39)	T59P	possibly damaging	Het
Pik3cg	A	G	12: 32,255,148 (GRCm39)	Y280H	probably damaging	Het
Pkd1l1	C	A	11: 8,784,773 (GRCm39)		probably null	Het
Plcd4	C	A	1: 74,591,274 (GRCm39)	T223N	probably damaging	Het
Polr1b	G	A	2: 128,967,829 (GRCm39)	G1074D	probably damaging	Het
Pou2f3	T	C	9: 43,040,188 (GRCm39)	T367A	probably damaging	Het
Prkdc	T	A	16: 15,617,790 (GRCm39)	M3207K	possibly damaging	Het
Rb1cc1	T	C	1: 6,319,730 (GRCm39)	S1050P	probably damaging	Het
Sf3b3	G	A	8: 111,540,383 (GRCm39)	R1013*	probably null	Het
Svep1	T	C	4: 58,068,988 (GRCm39)	T2933A	possibly damaging	Het
Vwf	A	G	6: 125,635,835 (GRCm39)	R289G	unknown	Het
Zfp263	T	C	16: 3,563,710 (GRCm39)	S155P	probably benign	Het

Other mutations in Pdgfra

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
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
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

2012-04-20