Incidental Mutation 'R6485:Pdgfra'
ID 517825
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 044617-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6485 (G1)
Quality Score 225.009
Status Not validated
Chromosome 5
Chromosomal Location 75312953-75358876 bp(+) (GRCm39)
Type of Mutation splice site (3 bp from exon)
DNA Base Change (assembly) A to T at 75335735 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000143906 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000000476] [ENSMUST00000168162] [ENSMUST00000201711] [ENSMUST00000202186] [ENSMUST00000202681]
AlphaFold P26618
Predicted Effect probably null
Transcript: ENSMUST00000000476
SMART Domains Protein: ENSMUSP00000000476
Gene: ENSMUSG00000029231

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 null
Transcript: ENSMUST00000168162
SMART Domains Protein: ENSMUSP00000127173
Gene: ENSMUSG00000029231

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 noncoding transcript
Transcript: ENSMUST00000183797
Predicted Effect probably null
Transcript: ENSMUST00000201711
SMART Domains Protein: ENSMUSP00000143891
Gene: ENSMUSG00000029231

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: ENSMUST00000202186
AA Change: Y456F

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000144543
Gene: ENSMUSG00000029231
AA Change: Y456F

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 null
Transcript: ENSMUST00000202681
SMART Domains Protein: ENSMUSP00000143906
Gene: ENSMUSG00000029231

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
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.5%
  • 10x: 97.7%
  • 20x: 93.1%
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: 39 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca16 C A 7: 120,026,390 (GRCm39) Y117* probably null Het
Acot5 A T 12: 84,122,258 (GRCm39) R281W probably damaging Het
Adamts20 T C 15: 94,241,852 (GRCm39) T719A probably benign Het
Arhgap33 T C 7: 30,223,429 (GRCm39) T867A probably benign Het
Bcl2a1c T C 9: 114,159,278 (GRCm39) Y19H probably benign Het
Bod1l A G 5: 41,974,459 (GRCm39) I2285T possibly damaging Het
Cacna2d1 A G 5: 16,559,655 (GRCm39) Y755C probably damaging Het
Cdc27 T C 11: 104,396,474 (GRCm39) T816A probably benign Het
Clasrp C A 7: 19,320,294 (GRCm39) probably benign Het
Col6a4 A G 9: 105,954,069 (GRCm39) probably null Het
Cpd T C 11: 76,699,533 (GRCm39) probably null Het
Crispld2 A G 8: 120,756,048 (GRCm39) D339G probably damaging Het
Dst A G 1: 34,333,610 (GRCm39) D7046G probably damaging Het
Erbin G T 13: 104,004,621 (GRCm39) Q136K probably damaging Het
Exph5 G A 9: 53,287,991 (GRCm39) E1691K possibly damaging Het
Fads6 A G 11: 115,176,264 (GRCm39) F187S probably benign Het
Foxg1 A T 12: 49,431,863 (GRCm39) I199F probably damaging Het
Garem1 T C 18: 21,262,894 (GRCm39) D640G probably benign Het
Gba2 A C 4: 43,574,118 (GRCm39) Y112D probably damaging Het
Gcfc2 T C 6: 81,916,528 (GRCm39) I323T probably damaging Het
Gm11595 G A 11: 99,663,381 (GRCm39) R100C unknown Het
Gria4 T A 9: 4,464,249 (GRCm39) Y571F probably damaging Het
Large2 T C 2: 92,196,373 (GRCm39) T485A probably benign Het
Lonrf1 A G 8: 36,696,288 (GRCm39) probably null Het
Mrgprb5 T C 7: 47,818,525 (GRCm39) N70S probably damaging Het
Muc2 T A 7: 141,300,473 (GRCm39) probably benign Het
Nol4 T C 18: 22,903,850 (GRCm39) D375G probably damaging Het
Or2b2 A G 13: 21,887,600 (GRCm39) Q143R probably benign Het
Pcnt G T 10: 76,225,164 (GRCm39) S1780* probably null Het
Pgd A T 4: 149,240,876 (GRCm39) probably null Het
Pla2g6 T C 15: 79,191,572 (GRCm39) I279V probably benign Het
Ptpn21 A T 12: 98,665,131 (GRCm39) C297* probably null Het
Ripply1 TTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT TTCCTCCTCCTCCTCCTCCTCCTCCTCCT X: 138,680,599 (GRCm39) probably benign Het
Rtcb T C 10: 85,793,508 (GRCm39) I22V probably benign Het
Slc25a30 G T 14: 76,012,447 (GRCm39) A67E probably damaging Het
Stk11ip T C 1: 75,506,612 (GRCm39) V605A possibly damaging Het
Ush1c A T 7: 45,858,534 (GRCm39) S585T probably benign Het
Vps13a T C 19: 16,657,414 (GRCm39) D1785G probably damaging Het
Zic5 T A 14: 122,697,052 (GRCm39) Y521F unknown 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
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
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'- AGAGACAAGAGCTGCTCTGC -3'
(R):5'- TAAAGGCCCTTTGAGGACATG -3'

Sequencing Primer
(F):5'- AAGAGCTGCTCTGCCCTGAC -3'
(R):5'- CAAGAGATGGAATCCACTTTCAG -3'
Posted On 2018-05-21