Incidental Mutation 'IGL01485:Pdgfra'
| ID |
88721 |
| Institutional Source |
Australian Phenomics Network
(link to record)
|
| Gene Symbol |
Pdgfra
|
| Ensembl Gene |
ENSMUSG00000029231 |
| Gene Name |
platelet derived growth factor receptor, alpha polypeptide |
| Synonyms |
Pdgfr-2, CD140a |
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
IGL01485
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
5 |
| Chromosomal Location |
75312953-75358876 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 75324313 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Asparagine
at position 56
(S56N)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000144634
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000000476]
[ENSMUST00000168162]
[ENSMUST00000200822]
[ENSMUST00000201711]
[ENSMUST00000202161]
[ENSMUST00000202186]
[ENSMUST00000202681]
[ENSMUST00000202992]
|
| AlphaFold |
P26618 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000000476
AA Change: S56N
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000000476
Gene: ENSMUSG00000029231
AA Change: S56N
| Domain | Start | End | E-Value | Type |
|---|
|
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: S56N
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000127173
Gene: ENSMUSG00000029231
AA Change: S56N
| Domain | Start | End | E-Value | Type |
|---|
|
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: ENSMUST00000200822
AA Change: S56N
PolyPhen 2
Score 0.024 (Sensitivity: 0.95; Specificity: 0.81)
|
| SMART Domains |
Protein: ENSMUSP00000144634
Gene: ENSMUSG00000029231
AA Change: S56N
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
23 |
N/A |
INTRINSIC |
|
IG
|
34 |
122 |
2.6e-5 |
SMART |
|
IG_like
|
135 |
206 |
7e-2 |
SMART |
|
Blast:IG
|
220 |
243 |
3e-6 |
BLAST |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000201241
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000201711
AA Change: S56N
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000143891
Gene: ENSMUSG00000029231
AA Change: S56N
| Domain | Start | End | E-Value | Type |
|---|
|
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: ENSMUST00000202161
AA Change: S56N
PolyPhen 2
Score 0.017 (Sensitivity: 0.95; Specificity: 0.80)
|
| SMART Domains |
Protein: ENSMUSP00000144485
Gene: ENSMUSG00000029231
AA Change: S56N
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
23 |
N/A |
INTRINSIC |
|
Blast:IG
|
34 |
88 |
5e-32 |
BLAST |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000202186
AA Change: S56N
PolyPhen 2
Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)
|
| SMART Domains |
Protein: ENSMUSP00000144543
Gene: ENSMUSG00000029231
AA Change: S56N
| Domain | Start | End | E-Value | Type |
|---|
|
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: S56N
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000143906
Gene: ENSMUSG00000029231
AA Change: S56N
| Domain | Start | End | E-Value | Type |
|---|
|
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: ENSMUST00000202992
AA Change: S56N
PolyPhen 2
Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
|
| SMART Domains |
Protein: ENSMUSP00000144132
Gene: ENSMUSG00000029231
AA Change: S56N
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
23 |
N/A |
INTRINSIC |
|
IG
|
34 |
122 |
2.6e-5 |
SMART |
|
| Coding Region Coverage |
|
| 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: 34 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4930590J08Rik |
C |
T |
6: 91,927,003 (GRCm39) |
L888F |
probably damaging |
Het |
| Aftph |
G |
T |
11: 20,642,507 (GRCm39) |
A842E |
probably damaging |
Het |
| Ankrd13d |
A |
T |
19: 4,323,592 (GRCm39) |
M257K |
probably benign |
Het |
| Anks1 |
T |
C |
17: 28,270,558 (GRCm39) |
F786L |
probably damaging |
Het |
| Cd2ap |
A |
T |
17: 43,163,365 (GRCm39) |
I20N |
probably damaging |
Het |
| Cdh20 |
C |
T |
1: 104,861,832 (GRCm39) |
T4M |
probably benign |
Het |
| Dnah5 |
C |
T |
15: 28,331,872 (GRCm39) |
R2153C |
probably damaging |
Het |
| Fap |
G |
A |
2: 62,374,655 (GRCm39) |
P248L |
possibly damaging |
Het |
| Hps4 |
T |
A |
5: 112,512,377 (GRCm39) |
|
probably benign |
Het |
| Igdcc4 |
C |
A |
9: 65,029,889 (GRCm39) |
T313K |
probably benign |
Het |
| Klhl30 |
G |
A |
1: 91,281,761 (GRCm39) |
V121I |
probably damaging |
Het |
| Ldb3 |
C |
A |
14: 34,264,519 (GRCm39) |
E526D |
probably damaging |
Het |
| Ldc1 |
T |
A |
4: 130,109,218 (GRCm39) |
Y274F |
probably benign |
Het |
| Lhfpl4 |
T |
A |
6: 113,171,082 (GRCm39) |
I35F |
probably benign |
Het |
| Lpin1 |
A |
G |
12: 16,612,358 (GRCm39) |
|
probably benign |
Het |
| Nek1 |
T |
A |
8: 61,502,860 (GRCm39) |
C436S |
probably benign |
Het |
| Nek5 |
C |
A |
8: 22,573,385 (GRCm39) |
A524S |
probably benign |
Het |
| Nkx2-3 |
C |
T |
19: 43,601,094 (GRCm39) |
T52M |
possibly damaging |
Het |
| Or1e33 |
A |
G |
11: 73,738,036 (GRCm39) |
I305T |
probably benign |
Het |
| Or2w2 |
A |
T |
13: 21,758,627 (GRCm39) |
|
probably null |
Het |
| Or8b56 |
G |
A |
9: 38,739,895 (GRCm39) |
V303I |
possibly damaging |
Het |
| Pappa |
T |
C |
4: 65,107,536 (GRCm39) |
V649A |
probably damaging |
Het |
| Parp4 |
T |
A |
14: 56,859,661 (GRCm39) |
Y920N |
possibly damaging |
Het |
| Pigg |
T |
C |
5: 108,484,067 (GRCm39) |
V438A |
possibly damaging |
Het |
| Ptn |
A |
T |
6: 36,720,298 (GRCm39) |
C85S |
probably damaging |
Het |
| Sh3rf1 |
A |
C |
8: 61,782,365 (GRCm39) |
E169A |
possibly damaging |
Het |
| Slc30a10 |
T |
A |
1: 185,187,616 (GRCm39) |
V119E |
probably damaging |
Het |
| Speg |
A |
G |
1: 75,364,471 (GRCm39) |
E178G |
probably damaging |
Het |
| Sspo |
A |
G |
6: 48,455,665 (GRCm39) |
Y3105C |
probably damaging |
Het |
| Supt3 |
A |
G |
17: 45,430,045 (GRCm39) |
E366G |
possibly damaging |
Het |
| Top2a |
A |
T |
11: 98,901,856 (GRCm39) |
L458Q |
probably damaging |
Het |
| Ttc21b |
G |
A |
2: 66,082,234 (GRCm39) |
|
probably benign |
Het |
| Usp24 |
T |
C |
4: 106,219,429 (GRCm39) |
F542L |
probably benign |
Het |
| Vmn1r234 |
T |
A |
17: 21,449,171 (GRCm39) |
D28E |
possibly damaging |
Het |
|
| Other mutations in Pdgfra |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH 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 |
|
|
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 |
|
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 |
|
| Posted On |
2013-11-18 |
Incidental Mutation