Incidental Mutation 'R1376:Pdgfd'
| ID |
186261 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Pdgfd
|
| Ensembl Gene |
ENSMUSG00000032006 |
| Gene Name |
platelet-derived growth factor, D polypeptide |
| Synonyms |
1110003I09Rik |
| MMRRC Submission |
039440-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.085)
|
| Stock # |
R1376 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
9 |
| Chromosomal Location |
6168584-6378850 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 6376994 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Valine
at position 357
(I357V)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000056240
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000058692]
[ENSMUST00000168039]
[ENSMUST00000214892]
|
| AlphaFold |
Q925I7 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000058692
AA Change: I357V
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
| SMART Domains |
Protein: ENSMUSP00000056240
Gene: ENSMUSG00000032006
AA Change: I357V
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
23 |
N/A |
INTRINSIC |
|
CUB
|
48 |
164 |
5.38e-25 |
SMART |
|
PDGF
|
265 |
358 |
4.58e-3 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000168039
AA Change: I363V
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000128388
Gene: ENSMUSG00000032006
AA Change: I363V
| Domain | Start | End | E-Value | Type |
|---|
|
signal peptide
|
1 |
23 |
N/A |
INTRINSIC |
|
CUB
|
54 |
170 |
5.38e-25 |
SMART |
|
PDGF
|
271 |
364 |
4.58e-3 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000214892
|
| Meta Mutation Damage Score |
0.0594 |
| Coding Region Coverage |
- 1x: 98.9%
- 3x: 97.9%
- 10x: 94.9%
- 20x: 89.2%
|
| Validation Efficiency |
100% (29/29) |
| 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: 34 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 5730455P16Rik |
A |
T |
11: 80,254,735 (GRCm39) |
I362N |
possibly damaging |
Het |
| 9130023H24Rik |
A |
G |
7: 127,836,182 (GRCm39) |
V137A |
probably benign |
Het |
| Adal |
A |
G |
2: 120,983,011 (GRCm39) |
D177G |
probably damaging |
Het |
| Cdcp2 |
G |
T |
4: 106,959,956 (GRCm39) |
V124F |
possibly damaging |
Het |
| Ceacam3 |
T |
C |
7: 16,897,088 (GRCm39) |
C685R |
probably damaging |
Het |
| Cep295 |
T |
C |
9: 15,252,164 (GRCm39) |
|
probably benign |
Het |
| Cfd |
T |
C |
10: 79,727,986 (GRCm39) |
I174T |
possibly damaging |
Het |
| Dapk2 |
C |
G |
9: 66,127,925 (GRCm39) |
R68G |
probably damaging |
Het |
| Ehd1 |
C |
T |
19: 6,344,418 (GRCm39) |
T226M |
probably damaging |
Het |
| Elp5 |
A |
G |
11: 69,865,916 (GRCm39) |
V120A |
probably benign |
Het |
| Fzd1 |
G |
A |
5: 4,807,174 (GRCm39) |
T136M |
possibly damaging |
Het |
| Galntl5 |
G |
T |
5: 25,391,286 (GRCm39) |
V62F |
probably benign |
Het |
| Gm11787 |
A |
G |
4: 3,516,373 (GRCm39) |
|
noncoding transcript |
Het |
| Josd2 |
C |
A |
7: 44,120,539 (GRCm39) |
P50H |
probably damaging |
Het |
| Lect2 |
T |
A |
13: 56,690,577 (GRCm39) |
I133F |
probably damaging |
Het |
| Lifr |
A |
G |
15: 7,214,245 (GRCm39) |
T700A |
probably benign |
Het |
| Lpl |
T |
C |
8: 69,340,250 (GRCm39) |
W82R |
probably damaging |
Het |
| Man2a1 |
C |
T |
17: 64,979,038 (GRCm39) |
R523C |
possibly damaging |
Het |
| Mast4 |
T |
C |
13: 102,872,916 (GRCm39) |
K1959E |
possibly damaging |
Het |
| Minar1 |
T |
C |
9: 89,473,299 (GRCm39) |
T871A |
probably damaging |
Het |
| Or10ag57 |
A |
G |
2: 87,218,162 (GRCm39) |
M38V |
probably benign |
Het |
| Or10ag58 |
C |
T |
2: 87,264,903 (GRCm39) |
S24L |
possibly damaging |
Het |
| Pde4dip |
A |
G |
3: 97,650,533 (GRCm39) |
V963A |
probably damaging |
Het |
| Pold1 |
T |
C |
7: 44,189,986 (GRCm39) |
D400G |
probably damaging |
Het |
| Ppp1r12a |
T |
C |
10: 108,034,779 (GRCm39) |
I108T |
probably damaging |
Het |
| Rimbp2 |
G |
C |
5: 128,847,355 (GRCm39) |
P931A |
possibly damaging |
Het |
| Rsf1 |
GCG |
GCGACG |
7: 97,229,114 (GRCm39) |
|
probably benign |
Homo |
| Sec24a |
A |
C |
11: 51,591,740 (GRCm39) |
|
probably benign |
Het |
| Sf3b1 |
A |
T |
1: 55,058,424 (GRCm39) |
V55E |
probably damaging |
Het |
| Sult2a2 |
T |
C |
7: 13,468,696 (GRCm39) |
V54A |
probably damaging |
Het |
| Taok3 |
T |
C |
5: 117,404,026 (GRCm39) |
Y734H |
probably damaging |
Het |
| Tasor |
A |
G |
14: 27,151,338 (GRCm39) |
K105E |
probably benign |
Het |
| Tuba3b |
A |
G |
6: 145,564,500 (GRCm39) |
E90G |
possibly damaging |
Het |
| Vmn2r115 |
ATCTTCT |
ATCT |
17: 23,578,962 (GRCm39) |
|
probably benign |
Het |
|
| Other mutations in Pdgfd |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH 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 |
|
R0122:Pdgfd
|
UTSW |
9 |
6,293,851 (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 |
|
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'- ACCCCTGCATGTTGCATGGTTAG -3'
(R):5'- TGGACAAGTGCCTTCTTTAAGTGAGC -3'
Sequencing Primer
(F):5'- TTACTCACTCATTACCAGAAGGGG -3'
(R):5'- GTGCCTTCTTTAAGTGAGCAAAATC -3'
|
| Posted On |
2014-05-09 |
Incidental Mutation