Incidental Mutation 'R6009:Pdgfa'
ID 479643
Institutional Source Beutler Lab
Gene Symbol Pdgfa
Ensembl Gene ENSMUSG00000025856
Gene Name platelet derived growth factor, alpha
Synonyms
MMRRC Submission 044186-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6009 (G1)
Quality Score 225.009
Status Validated
Chromosome 5
Chromosomal Location 138961769-138983125 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 138964954 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 176 (E176G)
Ref Sequence ENSEMBL: ENSMUSP00000106522 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046901] [ENSMUST00000076095] [ENSMUST00000110896] [ENSMUST00000110897]
AlphaFold no structure available at present
Predicted Effect probably damaging
Transcript: ENSMUST00000046901
AA Change: E176G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000038870
Gene: ENSMUSG00000025856
AA Change: E176G

DomainStartEndE-ValueType
signal peptide 1 20 N/A INTRINSIC
PDGF 94 181 1.5e-47 SMART
low complexity region 189 207 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000076095
AA Change: E176G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000075463
Gene: ENSMUSG00000025856
AA Change: E176G

DomainStartEndE-ValueType
signal peptide 1 20 N/A INTRINSIC
PDGF 94 181 2.98e-45 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000110896
AA Change: E176G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000106521
Gene: ENSMUSG00000025856
AA Change: E176G

DomainStartEndE-ValueType
signal peptide 1 20 N/A INTRINSIC
PDGF 94 181 2.98e-45 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000110897
AA Change: E176G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000106522
Gene: ENSMUSG00000025856
AA Change: E176G

DomainStartEndE-ValueType
signal peptide 1 20 N/A INTRINSIC
PDGF 94 181 2.98e-45 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000144934
Meta Mutation Damage Score 0.3679 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.5%
  • 10x: 97.3%
  • 20x: 91.5%
Validation Efficiency 100% (53/53)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the protein family comprised of both platelet-derived growth factors (PDGF) and vascular endothelial growth factors (VEGF). The encoded preproprotein is proteolytically processed to generate platelet-derived growth factor subunit A, which can homodimerize, or alternatively, heterodimerize with the related platelet-derived growth factor subunit B. These proteins bind and activate PDGF receptor tyrosine kinases, which play a role in a wide range of developmental processes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2015]
PHENOTYPE: Homozygotes for a targeted null mutation die either before E10.0 or postnatally. The latter exhibit lung emphysema, reduced numbers of oligodendrocytes, tremors, and abnormalities of the skin, hair follicles, and gastrointestinal lining. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 52 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Actr8 A G 14: 29,700,454 (GRCm39) probably benign Het
Afap1 T C 5: 36,154,904 (GRCm39) S683P probably damaging Het
Chid1 T A 7: 141,109,493 (GRCm39) D131V probably damaging Het
Clstn2 C T 9: 97,338,579 (GRCm39) R860Q probably benign Het
Crlf1 A C 8: 70,956,129 (GRCm39) K403T probably damaging Het
Ctdspl2 T G 2: 121,819,319 (GRCm39) N201K probably benign Het
Cyb561a3 G A 19: 10,564,172 (GRCm39) V171I possibly damaging Het
Dazap1 T C 10: 80,121,138 (GRCm39) probably benign Het
Dbf4 G T 5: 8,453,718 (GRCm39) Q235K probably damaging Het
Dgka C T 10: 128,559,548 (GRCm39) G471D probably damaging Het
Fam13b A T 18: 34,630,458 (GRCm39) F100Y possibly damaging Het
Flii A T 11: 60,611,583 (GRCm39) L376* probably null Het
Fnip1 G T 11: 54,393,097 (GRCm39) G487V probably damaging Het
Gm7247 C T 14: 51,601,805 (GRCm39) S26F probably benign Het
Golgb1 G T 16: 36,735,321 (GRCm39) A1523S probably damaging Het
Gstm4 A G 3: 107,950,659 (GRCm39) V114A possibly damaging Het
Gtf3c1 A G 7: 125,246,602 (GRCm39) F1569S possibly damaging Het
Gtf3c5 A T 2: 28,461,177 (GRCm39) D312E probably benign Het
Gtpbp1 G A 15: 79,596,297 (GRCm39) V149M probably damaging Het
Hoxa7 C T 6: 52,194,367 (GRCm39) V7M probably damaging Het
Il17f C T 1: 20,849,510 (GRCm39) probably null Het
Ints9 T C 14: 65,245,531 (GRCm39) V263A probably benign Het
Kansl1l C T 1: 66,774,759 (GRCm39) C689Y probably benign Het
Kctd7 G A 5: 130,174,039 (GRCm39) G39E probably damaging Het
Krt82 T A 15: 101,453,540 (GRCm39) D282V probably benign Het
Lemd1 G T 1: 132,155,990 (GRCm39) E11* probably null Het
Maml2 A G 9: 13,532,294 (GRCm39) T503A probably benign Het
Mief2 A G 11: 60,622,485 (GRCm39) T352A probably benign Het
Msantd1 C A 5: 35,075,049 (GRCm39) T37K probably benign Het
Mtus2 A G 5: 148,243,462 (GRCm39) E94G probably damaging Het
Naaa A T 5: 92,407,440 (GRCm39) L353Q probably benign Het
Nek5 T C 8: 22,610,838 (GRCm39) E55G probably benign Het
Npat T C 9: 53,474,749 (GRCm39) M847T probably damaging Het
Nus1 G A 10: 52,309,539 (GRCm39) V268I probably benign Het
Or51r1 A G 7: 102,227,801 (GRCm39) N33S possibly damaging Het
Parn C T 16: 13,485,428 (GRCm39) D23N probably damaging Het
Plcl1 T A 1: 55,735,405 (GRCm39) F249I probably damaging Het
Plscr5 C T 9: 92,086,488 (GRCm39) Q153* probably null Het
Polr2b T C 5: 77,468,099 (GRCm39) I133T probably benign Het
Polr3c A G 3: 96,620,930 (GRCm39) S463P probably damaging Het
Pprc1 A T 19: 46,060,171 (GRCm39) I1530L probably damaging Het
Prex1 C T 2: 166,423,904 (GRCm39) S996N probably damaging Het
Rnf169 C A 7: 99,576,330 (GRCm39) R291S possibly damaging Het
Setd5 A G 6: 113,087,480 (GRCm39) K127R probably damaging Het
Slc25a26 G T 6: 94,487,807 (GRCm39) V89L probably benign Het
Slc4a10 A G 2: 61,877,034 (GRCm39) T16A probably benign Het
Smchd1 A T 17: 71,747,951 (GRCm39) H430Q probably damaging Het
Ttll7 A T 3: 146,640,290 (GRCm39) D503V probably damaging Het
Vav2 A T 2: 27,161,912 (GRCm39) probably null Het
Zbtb47 T C 9: 121,591,937 (GRCm39) S86P possibly damaging Het
Zfp345 A T 2: 150,314,437 (GRCm39) C367S probably damaging Het
Zfp964 T A 8: 70,116,106 (GRCm39) H235Q possibly damaging Het
Other mutations in Pdgfa
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00329:Pdgfa APN 5 138,974,216 (GRCm39) splice site probably benign
IGL02219:Pdgfa APN 5 138,971,950 (GRCm39) missense probably damaging 1.00
R1852:Pdgfa UTSW 5 138,964,927 (GRCm39) missense probably benign 0.31
R3039:Pdgfa UTSW 5 138,972,114 (GRCm39) missense probably benign 0.10
R4368:Pdgfa UTSW 5 138,972,061 (GRCm39) missense probably damaging 1.00
R4647:Pdgfa UTSW 5 138,964,939 (GRCm39) missense probably benign 0.14
R4773:Pdgfa UTSW 5 138,979,051 (GRCm39) missense probably benign 0.03
R5262:Pdgfa UTSW 5 138,979,049 (GRCm39) missense probably benign 0.06
R5317:Pdgfa UTSW 5 138,974,102 (GRCm39) critical splice donor site probably null
R8446:Pdgfa UTSW 5 138,964,395 (GRCm39) missense unknown
R8992:Pdgfa UTSW 5 138,971,977 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- AAGCTAGTGTGGACAGCTGG -3'
(R):5'- AGCTCAAGGGAAGATGCCTTG -3'

Sequencing Primer
(F):5'- AAATCCAGGCCTGCTGACTTG -3'
(R):5'- ATGCCTTGAAGAGAGTTAGGTATC -3'
Posted On 2017-06-26