Incidental Mutation 'R5262:Pdgfa'
ID 401494
Institutional Source Beutler Lab
Gene Symbol Pdgfa
Ensembl Gene ENSMUSG00000025856
Gene Name platelet derived growth factor, alpha
Synonyms
MMRRC Submission 042857-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5262 (G1)
Quality Score 211
Status Validated
Chromosome 5
Chromosomal Location 138961769-138983125 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 138979049 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 52 (S52P)
Ref Sequence ENSEMBL: ENSMUSP00000038870 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046901] [ENSMUST00000076095] [ENSMUST00000110896] [ENSMUST00000110897]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000046901
AA Change: S52P

PolyPhen 2 Score 0.058 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000038870
Gene: ENSMUSG00000025856
AA Change: S52P

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 benign
Transcript: ENSMUST00000076095
AA Change: S52P

PolyPhen 2 Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000075463
Gene: ENSMUSG00000025856
AA Change: S52P

DomainStartEndE-ValueType
signal peptide 1 20 N/A INTRINSIC
PDGF 94 181 2.98e-45 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000100518
SMART Domains Protein: ENSMUSP00000098087
Gene: ENSMUSG00000075585

DomainStartEndE-ValueType
low complexity region 3 19 N/A INTRINSIC
low complexity region 67 99 N/A INTRINSIC
low complexity region 102 170 N/A INTRINSIC
low complexity region 202 227 N/A INTRINSIC
low complexity region 240 256 N/A INTRINSIC
low complexity region 269 282 N/A INTRINSIC
low complexity region 294 305 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000110896
AA Change: S52P

PolyPhen 2 Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000106521
Gene: ENSMUSG00000025856
AA Change: S52P

DomainStartEndE-ValueType
signal peptide 1 20 N/A INTRINSIC
PDGF 94 181 2.98e-45 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000110897
AA Change: S52P

PolyPhen 2 Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000106522
Gene: ENSMUSG00000025856
AA Change: S52P

DomainStartEndE-ValueType
signal peptide 1 20 N/A INTRINSIC
PDGF 94 181 2.98e-45 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000124080
Predicted Effect noncoding transcript
Transcript: ENSMUST00000132051
Predicted Effect noncoding transcript
Transcript: ENSMUST00000144934
Predicted Effect noncoding transcript
Transcript: ENSMUST00000187923
Meta Mutation Damage Score 0.1110 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.9%
  • 20x: 94.5%
Validation Efficiency 98% (61/62)
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: 54 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ago4 T A 4: 126,390,557 (GRCm39) D821V possibly damaging Het
Ankdd1b C A 13: 96,557,281 (GRCm39) R384L probably damaging Het
Ces1e A G 8: 93,950,586 (GRCm39) F65S probably damaging Het
Cfap53 A C 18: 74,462,530 (GRCm39) S425R probably benign Het
Corin A G 5: 72,462,298 (GRCm39) V837A probably damaging Het
Cyp2d34 A T 15: 82,502,572 (GRCm39) V188E probably damaging Het
Defb26 A T 2: 152,349,878 (GRCm39) M134K unknown Het
Dnah10 A C 5: 124,862,220 (GRCm39) K2158N probably damaging Het
Dnah9 C T 11: 66,003,159 (GRCm39) V882M probably benign Het
Dpyd C A 3: 118,591,071 (GRCm39) Y186* probably null Het
Elovl1 G A 4: 118,288,124 (GRCm39) probably benign Het
Fars2 T A 13: 36,526,001 (GRCm39) I329N probably damaging Het
Gstm1 T A 3: 107,923,679 (GRCm39) M109L probably benign Het
Gtf2e1 T C 16: 37,356,293 (GRCm39) T80A probably damaging Het
Gtf2h2 A G 13: 100,618,356 (GRCm39) probably benign Het
Hrh4 G T 18: 13,148,870 (GRCm39) L77F probably damaging Het
Ifi47 A G 11: 48,986,559 (GRCm39) T109A probably benign Het
Igsf5 G T 16: 96,192,237 (GRCm39) E179* probably null Het
Ints8 A G 4: 11,211,916 (GRCm39) I885T probably damaging Het
Iqgap1 T G 7: 80,376,490 (GRCm39) I1341L probably benign Het
Kmt2b A G 7: 30,269,219 (GRCm39) L2567P probably damaging Het
Lilrb4a T C 10: 51,369,303 (GRCm39) probably null Het
Maip1 G A 1: 57,446,131 (GRCm39) R67H probably damaging Het
Muc6 T A 7: 141,237,375 (GRCm39) I254F possibly damaging Het
Nfkb1 A T 3: 135,318,173 (GRCm39) probably null Het
Nlrp4a T C 7: 26,159,236 (GRCm39) probably null Het
Nrap A T 19: 56,308,655 (GRCm39) I1477N possibly damaging Het
Pou1f1 G T 16: 65,328,868 (GRCm39) E196* probably null Het
Ppp2r5e G A 12: 75,640,045 (GRCm39) R19W probably damaging Het
Ptn T A 6: 36,721,419 (GRCm39) Q7L probably benign Het
Rbp3 G T 14: 33,676,807 (GRCm39) A252S probably damaging Het
Rcor2 G T 19: 7,251,426 (GRCm39) V313L probably damaging Het
Rtp3 A T 9: 110,815,195 (GRCm39) probably benign Het
Ryr2 T C 13: 11,787,323 (GRCm39) T1017A probably damaging Het
Scgb2b11 T C 7: 31,908,776 (GRCm39) N108S probably benign Het
Sgo2b C A 8: 64,396,171 (GRCm39) L28F probably damaging Het
Shroom3 A G 5: 93,112,432 (GRCm39) E1850G probably damaging Het
Slc16a14 A G 1: 84,890,612 (GRCm39) L231P probably benign Het
Slfn5 A G 11: 82,847,496 (GRCm39) E127G possibly damaging Het
Snx16 C T 3: 10,502,892 (GRCm39) M118I probably damaging Het
Snx21 T C 2: 164,633,741 (GRCm39) F176L probably damaging Het
Tap2 A G 17: 34,432,990 (GRCm39) N424S probably benign Het
Tcf7l1 T C 6: 72,613,449 (GRCm39) probably benign Het
Trappc8 C T 18: 20,951,247 (GRCm39) V1400I probably benign Het
Trim58 T C 11: 58,542,494 (GRCm39) Y485H possibly damaging Het
U2af1l4 C T 7: 30,263,638 (GRCm39) T65I probably benign Het
Ufl1 G T 4: 25,251,294 (GRCm39) probably benign Het
Usp8 A G 2: 126,593,031 (GRCm39) N762S probably damaging Het
Virma A T 4: 11,539,926 (GRCm39) D1465V probably benign Het
Vmn1r48 A T 6: 90,013,016 (GRCm39) S270T probably benign Het
Vrk2 T A 11: 26,541,697 (GRCm39) Y9F possibly damaging Het
Wwp1 A G 4: 19,631,057 (GRCm39) F659L probably damaging Het
Zbtb24 C T 10: 41,340,556 (GRCm39) Q529* probably null Het
Zranb1 CTGATGATGATG CTGATGATGATGATG 7: 132,584,556 (GRCm39) probably benign 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
R5317:Pdgfa UTSW 5 138,974,102 (GRCm39) critical splice donor site probably null
R6009:Pdgfa UTSW 5 138,964,954 (GRCm39) missense probably damaging 1.00
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'- GAAACGCCTGACTCATACGC -3'
(R):5'- CATGTCAAGGCATTGTTGGG -3'

Sequencing Primer
(F):5'- TGACTCATACGCCTGGGC -3'
(R):5'- TCTAGGGCCTAACGAGGGTC -3'
Posted On 2016-07-06