Incidental Mutation 'R6141:Pdgfra'
ID 488573
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 044288-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6141 (G1)
Quality Score 225.009
Status Validated
Chromosome 5
Chromosomal Location 75312953-75358876 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 75334057 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Glycine at position 377 (S377G)
Ref Sequence ENSEMBL: ENSMUSP00000144543 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000000476] [ENSMUST00000168162] [ENSMUST00000201711] [ENSMUST00000202186] [ENSMUST00000202681]
AlphaFold P26618
Predicted Effect probably benign
Transcript: ENSMUST00000000476
AA Change: S377G

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000000476
Gene: ENSMUSG00000029231
AA Change: S377G

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: S377G

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000127173
Gene: ENSMUSG00000029231
AA Change: S377G

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 benign
Transcript: ENSMUST00000201711
AA Change: S377G

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000143891
Gene: ENSMUSG00000029231
AA Change: S377G

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 damaging
Transcript: ENSMUST00000202186
AA Change: S377G

PolyPhen 2 Score 0.978 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000144543
Gene: ENSMUSG00000029231
AA Change: S377G

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: S377G

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000143906
Gene: ENSMUSG00000029231
AA Change: S377G

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
Meta Mutation Damage Score 0.1849 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.3%
  • 20x: 95.2%
Validation Efficiency 100% (51/51)
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: 50 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4933421I07Rik A T 7: 42,097,483 (GRCm39) C4S probably damaging Het
Abhd5 A T 9: 122,206,998 (GRCm39) T95S probably benign Het
Ambra1 A T 2: 91,706,099 (GRCm39) N795Y probably damaging Het
Brca2 A G 5: 150,464,102 (GRCm39) N1289D possibly damaging Het
Cavin2 T C 1: 51,340,097 (GRCm39) L258P probably damaging Het
Ccdc110 A G 8: 46,394,807 (GRCm39) T233A possibly damaging Het
Ccdc14 T A 16: 34,526,932 (GRCm39) I279N probably damaging Het
Cntn5 A T 9: 10,144,162 (GRCm39) L169Q probably benign Het
Dbf4 T C 5: 8,458,545 (GRCm39) S157G possibly damaging Het
Defb22 A T 2: 152,327,722 (GRCm39) N154K unknown Het
Eepd1 T A 9: 25,394,280 (GRCm39) D181E probably benign Het
Etfa T C 9: 55,372,103 (GRCm39) H286R probably damaging Het
Gm44419 T A 6: 65,127,940 (GRCm39) noncoding transcript Het
Gpatch4 C T 3: 87,962,047 (GRCm39) R155* probably null Het
Grik1 T G 16: 87,693,760 (GRCm39) R862S probably benign Het
Hectd1 A C 12: 51,792,875 (GRCm39) probably null Het
Ift122 T C 6: 115,892,972 (GRCm39) W919R probably damaging Het
Iqgap2 A T 13: 95,858,194 (GRCm39) probably null Het
Kcnq4 A T 4: 120,573,066 (GRCm39) I245N probably damaging Het
Map3k3 G T 11: 105,987,874 (GRCm39) R21L probably benign Het
Mllt10 T C 2: 18,215,604 (GRCm39) V1063A probably damaging Het
Msr1 A T 8: 40,084,360 (GRCm39) V65E probably damaging Het
Myom2 A T 8: 15,113,903 (GRCm39) D17V probably damaging Het
Naaladl1 T A 19: 6,159,785 (GRCm39) probably null Het
Naip6 T C 13: 100,444,741 (GRCm39) Y239C possibly damaging Het
Nckap1 C A 2: 80,360,551 (GRCm39) D533Y probably damaging Het
Ndufs2 T C 1: 171,064,185 (GRCm39) E375G probably damaging Het
Nsd1 T C 13: 55,439,097 (GRCm39) V1605A probably damaging Het
Or4k42 A G 2: 111,320,464 (GRCm39) I13T probably benign Het
Or52ae9 C A 7: 103,389,994 (GRCm39) R151L probably damaging Het
Or5ac17 T A 16: 59,036,916 (GRCm39) H20L probably benign Het
Or5b114-ps1 A T 19: 13,352,647 (GRCm39) Y107F probably benign Het
Or7e176 T A 9: 20,171,754 (GRCm39) M206K probably benign Het
Pcp2 G A 8: 3,673,543 (GRCm39) probably null Het
Reep5 A T 18: 34,505,511 (GRCm39) Y53* probably null Het
Ric1 T C 19: 29,572,842 (GRCm39) S761P probably damaging Het
Satb1 T C 17: 52,082,404 (GRCm39) T417A possibly damaging Het
Slc1a7 T A 4: 107,859,379 (GRCm39) M156K possibly damaging Het
Slc4a10 A G 2: 62,041,789 (GRCm39) E123G probably damaging Het
Slc66a1 A G 4: 139,027,556 (GRCm39) V262A probably benign Het
Snupn C A 9: 56,890,108 (GRCm39) Q310K possibly damaging Het
Stard13 A T 5: 150,965,707 (GRCm39) V916E probably damaging Het
Tlr1 T C 5: 65,082,556 (GRCm39) R674G possibly damaging Het
Tnfsf11 A G 14: 78,545,299 (GRCm39) Y11H probably damaging Het
Tnr T A 1: 159,714,692 (GRCm39) V857E probably benign Het
Tubgcp5 A G 7: 55,456,526 (GRCm39) I373V probably benign Het
Ush2a A T 1: 188,090,160 (GRCm39) R414S possibly damaging Het
Vmn2r100 T C 17: 19,742,576 (GRCm39) S317P probably benign Het
Wdr49 A T 3: 75,230,989 (GRCm39) F558I probably benign Het
Zfyve16 A G 13: 92,648,105 (GRCm39) I983T 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
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
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'- GAGGTCTTGCCAGAATTGTTAGC -3'
(R):5'- TTCTCCTCCAAGGCTTTGAAGAG -3'

Sequencing Primer
(F):5'- GGCTATGAGTGACACCTTCAATG -3'
(R):5'- TCCTCCAAGGCTTTGAAGAGAAGAG -3'
Posted On 2017-10-10