Incidental Mutation 'R0122:Pdgfd'
ID 21098
Institutional Source Beutler Lab
Gene Symbol Pdgfd
Ensembl Gene ENSMUSG00000032006
Gene Name platelet-derived growth factor, D polypeptide
Synonyms 1110003I09Rik
MMRRC Submission 038407-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.085) question?
Stock # R0122 (G1)
Quality Score 225
Status Validated (trace)
Chromosome 9
Chromosomal Location 6168584-6378850 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 6293851 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 142 (S142P)
Ref Sequence ENSEMBL: ENSMUSP00000149162 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000058692] [ENSMUST00000168039] [ENSMUST00000214892]
AlphaFold Q925I7
Predicted Effect probably damaging
Transcript: ENSMUST00000058692
AA Change: S136P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000056240
Gene: ENSMUSG00000032006
AA Change: S136P

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
CUB 48 164 5.38e-25 SMART
PDGF 265 358 4.58e-3 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000168039
AA Change: S142P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000128388
Gene: ENSMUSG00000032006
AA Change: S142P

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
CUB 54 170 5.38e-25 SMART
PDGF 271 364 4.58e-3 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000214892
AA Change: S142P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
Meta Mutation Damage Score 0.9497 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.2%
  • 10x: 95.9%
  • 20x: 91.3%
Validation Efficiency 99% (78/79)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a member of the platelet-derived growth factor family. The four members of this family are mitogenic factors for cells of mesenchymal origin and are characterized by a core motif of eight cysteines, seven of which are found in this factor. This gene product only forms homodimers and, therefore, does not dimerize with the other three family members. It differs from alpha and beta members of this family in having an unusual N-terminal domain, the CUB domain. Two splice variants have been identified for this gene. [provided by RefSeq, Jul 2008]
Allele List at MGI
Other mutations in this stock
Total: 74 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2010315B03Rik T C 9: 124,057,789 (GRCm39) probably benign Het
Adam12 T A 7: 133,614,077 (GRCm39) I60F probably benign Het
Adamts10 A G 17: 33,747,454 (GRCm39) probably benign Het
Adamts12 C T 15: 11,215,710 (GRCm39) R244C probably damaging Het
Adamts7 A G 9: 90,061,474 (GRCm39) E360G probably damaging Het
Atn1 A T 6: 124,720,197 (GRCm39) probably benign Het
Avl9 G T 6: 56,713,468 (GRCm39) R242L probably benign Het
Baz2b G T 2: 59,743,963 (GRCm39) probably null Het
Bloc1s6 G C 2: 122,587,963 (GRCm39) probably benign Het
Btbd9 C T 17: 30,493,916 (GRCm39) D492N possibly damaging Het
C1qa T A 4: 136,625,142 (GRCm39) T3S probably benign Het
Cacna1e A T 1: 154,319,647 (GRCm39) F1351Y probably damaging Het
Car9 C T 4: 43,512,206 (GRCm39) A356V probably benign Het
Ccdc116 T A 16: 16,960,598 (GRCm39) D73V probably damaging Het
Ces2g T C 8: 105,694,932 (GRCm39) Y518H probably damaging Het
Ciz1 A G 2: 32,261,431 (GRCm39) probably benign Het
Cmc1 A T 9: 117,894,388 (GRCm39) C29S probably damaging Het
Coil T A 11: 88,875,833 (GRCm39) probably benign Het
Col3a1 C T 1: 45,380,057 (GRCm39) probably benign Het
Cox15 A G 19: 43,737,229 (GRCm39) I135T possibly damaging Het
Cyld T C 8: 89,468,920 (GRCm39) S564P probably damaging Het
Dnah5 T A 15: 28,378,509 (GRCm39) N2948K probably damaging Het
Dnah7a G A 1: 53,436,301 (GRCm39) R4014W probably damaging Het
Dnmt3b T C 2: 153,518,618 (GRCm39) Y594H probably damaging Het
Dntt A G 19: 41,041,477 (GRCm39) K387R possibly damaging Het
Efcab7 G A 4: 99,749,560 (GRCm39) probably benign Het
Flvcr1 G T 1: 190,753,423 (GRCm39) P250T possibly damaging Het
Gga2 C A 7: 121,590,797 (GRCm39) V504L probably damaging Het
Gm12239 T A 11: 55,906,738 (GRCm39) noncoding transcript Het
Gm6327 T C 16: 12,578,890 (GRCm39) noncoding transcript Het
Krt26 G T 11: 99,224,545 (GRCm39) Y324* probably null Het
Lamb2 A T 9: 108,363,713 (GRCm39) H939L probably benign Het
Lipo3 C T 19: 33,600,086 (GRCm39) probably benign Het
Mmp1b G A 9: 7,386,689 (GRCm39) T145M probably damaging Het
Mrps27 G T 13: 99,501,736 (GRCm39) V76L probably benign Het
Mup6 T A 4: 60,003,995 (GRCm39) Y29* probably null Het
Nlrc3 T C 16: 3,776,822 (GRCm39) K756E probably damaging Het
Nnt T C 13: 119,505,133 (GRCm39) H527R probably damaging Het
Nudt8 T C 19: 4,051,306 (GRCm39) V59A probably benign Het
Ofcc1 A T 13: 40,434,032 (GRCm39) probably null Het
Or10d1 A T 9: 39,484,020 (GRCm39) D178E probably damaging Het
Or2a25 T C 6: 42,888,889 (GRCm39) V144A probably benign Het
Or51q1c T C 7: 103,652,565 (GRCm39) W28R probably damaging Het
Pias4 G T 10: 80,992,921 (GRCm39) Q22K probably damaging Het
Pin1 T C 9: 20,573,600 (GRCm39) I95T probably benign Het
Pramel23 A T 4: 143,424,974 (GRCm39) D156E probably benign Het
Prickle2 G A 6: 92,388,326 (GRCm39) Q359* probably null Het
Qrich2 G T 11: 116,337,639 (GRCm39) Q1950K possibly damaging Het
Rab10 C A 12: 3,359,357 (GRCm39) G21V probably damaging Het
Rbm27 T A 18: 42,447,033 (GRCm39) probably benign Het
Samd4 C A 14: 47,254,017 (GRCm39) S160R probably benign Het
Scube3 A C 17: 28,385,502 (GRCm39) probably benign Het
Serpinf2 A G 11: 75,327,372 (GRCm39) L185P probably damaging Het
Slc16a12 A G 19: 34,652,264 (GRCm39) I294T probably benign Het
Slc45a3 T A 1: 131,905,478 (GRCm39) M167K probably damaging Het
Sspo T A 6: 48,450,910 (GRCm39) L2673Q possibly damaging Het
Supt3 A G 17: 45,314,028 (GRCm39) D139G probably damaging Het
Tas1r3 T C 4: 155,945,290 (GRCm39) M644V probably benign Het
Tgfbi A G 13: 56,775,781 (GRCm39) T276A probably damaging Het
Tmem177 T C 1: 119,838,308 (GRCm39) I124V probably benign Het
Tmprss11f G T 5: 86,681,484 (GRCm39) probably benign Het
Tmprss3 G A 17: 31,412,876 (GRCm39) probably benign Het
Twf1 A G 15: 94,484,430 (GRCm39) probably benign Het
Uba52 T A 8: 70,961,951 (GRCm39) Q166L probably damaging Het
Ubr3 G T 2: 69,809,756 (GRCm39) G1242V probably damaging Het
Unc13d C T 11: 115,956,308 (GRCm39) S835N probably benign Het
Ush2a A G 1: 188,680,652 (GRCm39) K4877E possibly damaging Het
Vmn2r98 A G 17: 19,286,662 (GRCm39) I387V probably benign Het
Vps11 A T 9: 44,265,809 (GRCm39) I490N probably damaging Het
Vstm4 T A 14: 32,585,768 (GRCm39) probably null Het
Zfp110 C A 7: 12,582,524 (GRCm39) H391N possibly damaging Het
Zfp212 C T 6: 47,907,957 (GRCm39) P312L possibly damaging Het
Zfp329 A T 7: 12,544,914 (GRCm39) H203Q probably damaging Het
Zscan12 G A 13: 21,553,139 (GRCm39) G321E probably damaging Het
Other mutations in Pdgfd
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00545:Pdgfd APN 9 6,288,621 (GRCm39) nonsense probably null
IGL00806:Pdgfd APN 9 6,288,667 (GRCm39) missense probably benign 0.00
IGL01481:Pdgfd APN 9 6,337,271 (GRCm39) missense probably null 0.62
IGL01704:Pdgfd APN 9 6,337,327 (GRCm39) missense probably damaging 1.00
IGL02951:Pdgfd APN 9 6,288,494 (GRCm39) missense probably damaging 1.00
IGL03022:Pdgfd APN 9 6,288,495 (GRCm39) missense probably damaging 1.00
R0408:Pdgfd UTSW 9 6,293,928 (GRCm39) nonsense probably null
R0542:Pdgfd UTSW 9 6,359,769 (GRCm39) missense probably damaging 1.00
R0701:Pdgfd UTSW 9 6,359,706 (GRCm39) missense probably damaging 0.98
R1376:Pdgfd UTSW 9 6,376,994 (GRCm39) missense probably benign 0.00
R1376:Pdgfd UTSW 9 6,376,994 (GRCm39) missense probably benign 0.00
R1563:Pdgfd UTSW 9 6,293,939 (GRCm39) critical splice donor site probably null
R2513:Pdgfd UTSW 9 6,359,894 (GRCm39) missense probably damaging 1.00
R3751:Pdgfd UTSW 9 6,337,447 (GRCm39) splice site probably benign
R3831:Pdgfd UTSW 9 6,359,762 (GRCm39) missense probably damaging 1.00
R3832:Pdgfd UTSW 9 6,359,762 (GRCm39) missense probably damaging 1.00
R3833:Pdgfd UTSW 9 6,359,762 (GRCm39) missense probably damaging 1.00
R4691:Pdgfd UTSW 9 6,288,556 (GRCm39) missense probably damaging 1.00
R6280:Pdgfd UTSW 9 6,288,627 (GRCm39) missense probably benign 0.00
R6622:Pdgfd UTSW 9 6,293,818 (GRCm39) missense probably damaging 1.00
R7488:Pdgfd UTSW 9 6,359,739 (GRCm39) missense probably damaging 1.00
R7581:Pdgfd UTSW 9 6,293,894 (GRCm39) missense probably damaging 1.00
R7873:Pdgfd UTSW 9 6,337,271 (GRCm39) missense probably benign 0.06
R7883:Pdgfd UTSW 9 6,293,939 (GRCm39) critical splice donor site probably null
R8498:Pdgfd UTSW 9 6,288,655 (GRCm39) missense probably damaging 1.00
R8788:Pdgfd UTSW 9 6,377,000 (GRCm39) missense probably benign 0.00
R9147:Pdgfd UTSW 9 6,333,328 (GRCm39) missense probably benign 0.09
R9148:Pdgfd UTSW 9 6,333,328 (GRCm39) missense probably benign 0.09
R9386:Pdgfd UTSW 9 6,293,903 (GRCm39) missense possibly damaging 0.81
R9747:Pdgfd UTSW 9 6,337,310 (GRCm39) missense probably benign 0.09
RF009:Pdgfd UTSW 9 6,288,624 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GTGACTACTGGGGCATGTATCTCAAC -3'
(R):5'- CACTGGTTTTCCTTACAAACACAGGC -3'

Sequencing Primer
(F):5'- GGGGCATGTATCTCAACCTATC -3'
(R):5'- CTTTAAGATTCTGTCCAGAGGGAAG -3'
Posted On 2013-04-11