Incidental Mutation 'R5836:Pdgfra'
ID 449584
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 043222-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5836 (G1)
Quality Score 225
Status Not validated
Chromosome 5
Chromosomal Location 75312953-75358876 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 75324435 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tryptophan to Arginine at position 97 (W97R)
Ref Sequence ENSEMBL: ENSMUSP00000144543 (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: W97R

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000000476
Gene: ENSMUSG00000029231
AA Change: W97R

DomainStartEndE-ValueType
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: W97R

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000127173
Gene: ENSMUSG00000029231
AA Change: W97R

DomainStartEndE-ValueType
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: W97R

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000144634
Gene: ENSMUSG00000029231
AA Change: W97R

DomainStartEndE-ValueType
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: W97R

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000143891
Gene: ENSMUSG00000029231
AA Change: W97R

DomainStartEndE-ValueType
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
SMART Domains Protein: ENSMUSP00000144485
Gene: ENSMUSG00000029231

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
Blast:IG 34 88 5e-32 BLAST
Predicted Effect possibly damaging
Transcript: ENSMUST00000202186
AA Change: W97R

PolyPhen 2 Score 0.524 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000144543
Gene: ENSMUSG00000029231
AA Change: W97R

DomainStartEndE-ValueType
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: W97R

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000143906
Gene: ENSMUSG00000029231
AA Change: W97R

DomainStartEndE-ValueType
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: W97R

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000144132
Gene: ENSMUSG00000029231
AA Change: W97R

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
IG 34 122 2.6e-5 SMART
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.2%
  • 20x: 94.9%
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
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcf1 G T 17: 36,272,918 (GRCm39) A243D possibly damaging Het
Azin2 C T 4: 128,842,670 (GRCm39) G128D probably damaging Het
Babam1 A G 8: 71,855,687 (GRCm39) E260G probably benign Het
Brwd1 A T 16: 95,865,958 (GRCm39) S275T probably damaging Het
Cd8a T C 6: 71,350,775 (GRCm39) V80A possibly damaging Het
Clec4a3 T C 6: 122,929,861 (GRCm39) F12S possibly damaging Het
Dennd2b A T 7: 109,140,552 (GRCm39) S225T possibly damaging Het
Dnah5 A C 15: 28,383,738 (GRCm39) N2987H probably damaging Het
Dock9 A G 14: 121,918,763 (GRCm39) F78S probably damaging Het
Eml3 A G 19: 8,918,659 (GRCm39) T885A possibly damaging Het
Esr1 T C 10: 4,662,817 (GRCm39) V145A probably benign Het
Gm5108 A G 5: 68,101,953 (GRCm39) probably benign Het
Gpr179 T C 11: 97,229,882 (GRCm39) S758G probably benign Het
Heatr1 T A 13: 12,423,617 (GRCm39) L538Q probably damaging Het
Ikzf2 A G 1: 69,578,546 (GRCm39) I176T probably damaging Het
Lrp3 A G 7: 34,902,747 (GRCm39) V533A probably damaging Het
Nkx2-5 A T 17: 27,058,063 (GRCm39) V297E possibly damaging Het
Or13a19 G A 7: 139,902,827 (GRCm39) V72I probably benign Het
Or2y16 T C 11: 49,335,353 (GRCm39) L225P probably damaging Het
Or8g23 T C 9: 38,971,918 (GRCm39) T15A probably benign Het
Pclo T A 5: 14,728,549 (GRCm39) probably benign Het
Plekha5 T C 6: 140,372,250 (GRCm39) Y67H probably damaging Het
Plin5 A T 17: 56,422,549 (GRCm39) probably null Het
Pramel11 A G 4: 143,623,490 (GRCm39) V228A probably benign Het
Prickle1 T A 15: 93,400,898 (GRCm39) K529* probably null Het
Ptbp2 G A 3: 119,519,746 (GRCm39) T107I probably damaging Het
Ptpn12 C T 5: 21,214,544 (GRCm39) W197* probably null Het
Rhobtb1 T C 10: 69,105,819 (GRCm39) V128A probably damaging Het
Ryr2 T C 13: 11,618,618 (GRCm39) T3866A probably damaging Het
Serpina3m T C 12: 104,355,509 (GRCm39) Y59H probably damaging Het
Slc12a6 T C 2: 112,172,343 (GRCm39) V414A possibly damaging Het
Slc34a1 T C 13: 55,561,278 (GRCm39) M581T probably benign Het
Slco1c1 A G 6: 141,515,040 (GRCm39) Y596C probably damaging Het
Stoml1 T C 9: 58,168,123 (GRCm39) L278P probably benign Het
Tecpr2 C T 12: 110,897,945 (GRCm39) A399V possibly damaging Het
Tmem229a T C 6: 24,955,016 (GRCm39) E246G probably damaging Het
Vmn1r224 A T 17: 20,639,953 (GRCm39) I177L probably benign Het
Zswim5 C T 4: 116,842,000 (GRCm39) T860I probably benign Het
Other mutations in Pdgfra
AlleleSourceChrCoordTypePredicted EffectPPH 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
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
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'- AAGATTGTGCAGCTGAATTCGTC -3'
(R):5'- AGAAGGGAAAGACTTTTCTACCTTG -3'

Sequencing Primer
(F):5'- GAATTCGTCCTTTTCTCTGAGATGCG -3'
(R):5'- CCTTGCAAATTTCTCTGCAATAAAC -3'
Posted On 2016-12-20