Incidental Mutation 'R4165:Prdm1'
| ID |
321700 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Prdm1
|
| Ensembl Gene |
ENSMUSG00000038151 |
| Gene Name |
PR domain containing 1, with ZNF domain |
| Synonyms |
Blimp-1, PRDI-BF1, Blimp1, b2b1765Clo |
| MMRRC Submission |
041007-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R4165 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
10 |
| Chromosomal Location |
44313173-44404497 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 44317572 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Phenylalanine
at position 417
(Y417F)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000101129
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000039174]
[ENSMUST00000105490]
[ENSMUST00000218369]
|
| AlphaFold |
Q60636 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000039174
AA Change: Y450F
PolyPhen 2
Score 0.044 (Sensitivity: 0.94; Specificity: 0.83)
|
| SMART Domains |
Protein: ENSMUSP00000039248
Gene: ENSMUSG00000038151
AA Change: Y450F
| Domain | Start | End | E-Value | Type |
|---|
|
SET
|
118 |
239 |
1.1e-19 |
SMART |
|
low complexity region
|
359 |
393 |
N/A |
INTRINSIC |
|
low complexity region
|
541 |
556 |
N/A |
INTRINSIC |
|
ZnF_C2H2
|
606 |
628 |
6.42e-4 |
SMART |
|
ZnF_C2H2
|
634 |
656 |
3.89e-3 |
SMART |
|
ZnF_C2H2
|
662 |
684 |
7.26e-3 |
SMART |
|
ZnF_C2H2
|
690 |
712 |
1.36e-2 |
SMART |
|
ZnF_C2H2
|
718 |
738 |
1.12e2 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000105490
AA Change: Y417F
PolyPhen 2
Score 0.107 (Sensitivity: 0.93; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000101129
Gene: ENSMUSG00000038151
AA Change: Y417F
| Domain | Start | End | E-Value | Type |
|---|
|
SET
|
85 |
206 |
1.1e-19 |
SMART |
|
low complexity region
|
326 |
360 |
N/A |
INTRINSIC |
|
low complexity region
|
508 |
523 |
N/A |
INTRINSIC |
|
ZnF_C2H2
|
573 |
595 |
6.42e-4 |
SMART |
|
ZnF_C2H2
|
601 |
623 |
3.89e-3 |
SMART |
|
ZnF_C2H2
|
629 |
651 |
7.26e-3 |
SMART |
|
ZnF_C2H2
|
657 |
679 |
1.36e-2 |
SMART |
|
ZnF_C2H2
|
685 |
705 |
1.12e2 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000218369
AA Change: Y432F
PolyPhen 2
Score 0.074 (Sensitivity: 0.93; Specificity: 0.85)
|
| Meta Mutation Damage Score |
0.1514 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.8%
- 10x: 97.6%
- 20x: 96.1%
|
| Validation Efficiency |
97% (38/39) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that acts as a repressor of beta-interferon gene expression. The protein binds specifically to the PRDI (positive regulatory domain I element) of the beta-IFN gene promoter. Transcription of this gene increases upon virus induction. Two alternatively spliced transcript variants that encode different isoforms have been reported. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous null mice display embryonic lethality and impaired primordial germ cell development, while heterozygotes display a decreased numbers of primordial germ cells but normal migration. Conditional mutants display impaired plasma cell and pre-plasmamemory B cell development. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 38 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aak1 |
T |
A |
6: 86,827,044 (GRCm39) |
F4I |
probably damaging |
Het |
| Adamts8 |
G |
T |
9: 30,862,684 (GRCm39) |
E296D |
probably benign |
Het |
| Alg11 |
T |
C |
8: 22,555,573 (GRCm39) |
V278A |
probably damaging |
Het |
| Ankfy1 |
G |
A |
11: 72,605,310 (GRCm39) |
|
probably null |
Het |
| Avil |
C |
T |
10: 126,842,496 (GRCm39) |
Q92* |
probably null |
Het |
| Cfap300 |
A |
T |
9: 8,026,071 (GRCm39) |
L167Q |
probably damaging |
Het |
| CK137956 |
A |
T |
4: 127,864,522 (GRCm39) |
S36T |
possibly damaging |
Het |
| Epb41l3 |
T |
C |
17: 69,514,883 (GRCm39) |
S7P |
probably damaging |
Het |
| Espl1 |
A |
G |
15: 102,221,424 (GRCm39) |
I944V |
probably damaging |
Het |
| Fsd2 |
T |
C |
7: 81,195,608 (GRCm39) |
T434A |
probably damaging |
Het |
| Gm5174 |
A |
G |
10: 86,492,797 (GRCm39) |
|
noncoding transcript |
Het |
| Gpaa1 |
A |
C |
15: 76,216,667 (GRCm39) |
|
probably benign |
Het |
| Grina |
T |
A |
15: 76,133,529 (GRCm39) |
L334Q |
probably damaging |
Het |
| Gvin-ps5 |
T |
A |
7: 105,929,895 (GRCm39) |
|
noncoding transcript |
Het |
| Igkv15-103 |
G |
T |
6: 68,414,824 (GRCm39) |
G88* |
probably null |
Het |
| Ip6k2 |
G |
A |
9: 108,682,847 (GRCm39) |
R319Q |
probably benign |
Het |
| Kdm3b |
A |
T |
18: 34,928,797 (GRCm39) |
I183F |
probably benign |
Het |
| Kyat3 |
A |
G |
3: 142,432,066 (GRCm39) |
|
probably null |
Het |
| Larp7 |
A |
G |
3: 127,330,611 (GRCm39) |
Y569H |
probably benign |
Het |
| Loxhd1 |
A |
T |
18: 77,460,025 (GRCm39) |
I758F |
probably damaging |
Het |
| Nr1d2 |
T |
C |
14: 18,215,446 (GRCm38) |
I189V |
probably benign |
Het |
| Odad2 |
A |
T |
18: 7,217,008 (GRCm39) |
I668K |
probably damaging |
Het |
| Pcdhb19 |
T |
A |
18: 37,632,243 (GRCm39) |
N679K |
probably benign |
Het |
| Pigr |
G |
A |
1: 130,769,554 (GRCm39) |
D122N |
probably benign |
Het |
| Prap1 |
T |
A |
7: 139,676,091 (GRCm39) |
V35E |
probably benign |
Het |
| Ralgapa1 |
C |
T |
12: 55,687,429 (GRCm39) |
R2019Q |
probably damaging |
Het |
| Rps3 |
T |
C |
7: 99,132,816 (GRCm39) |
I5V |
probably benign |
Het |
| Sema3a |
A |
T |
5: 13,523,364 (GRCm39) |
|
probably null |
Het |
| Serpina3g |
A |
T |
12: 104,206,546 (GRCm39) |
T116S |
probably benign |
Het |
| Skint11 |
C |
A |
4: 114,101,856 (GRCm39) |
Q99K |
probably benign |
Het |
| Slc22a28 |
A |
G |
19: 8,040,773 (GRCm39) |
S493P |
possibly damaging |
Het |
| Snapc1 |
G |
T |
12: 74,029,354 (GRCm39) |
|
probably null |
Het |
| Sobp |
C |
T |
10: 42,897,644 (GRCm39) |
G647D |
probably damaging |
Het |
| Tomm22 |
C |
A |
15: 79,555,206 (GRCm39) |
|
probably benign |
Het |
| Trappc11 |
T |
C |
8: 47,978,003 (GRCm39) |
|
probably benign |
Het |
| Txnl4a |
T |
A |
18: 80,265,471 (GRCm39) |
M112K |
probably benign |
Het |
| Vmn2r16 |
T |
C |
5: 109,478,427 (GRCm39) |
F61L |
possibly damaging |
Het |
| Zfp709 |
C |
T |
8: 72,644,649 (GRCm39) |
Q693* |
probably null |
Het |
|
| Other mutations in Prdm1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00657:Prdm1
|
APN |
10 |
44,317,888 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01331:Prdm1
|
APN |
10 |
44,317,970 (GRCm39) |
missense |
possibly damaging |
0.67 |
|
IGL02064:Prdm1
|
APN |
10 |
44,317,338 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02669:Prdm1
|
APN |
10 |
44,315,880 (GRCm39) |
missense |
probably benign |
0.28 |
|
IGL02944:Prdm1
|
APN |
10 |
44,317,807 (GRCm39) |
missense |
probably benign |
|
|
IGL03295:Prdm1
|
APN |
10 |
44,315,866 (GRCm39) |
missense |
probably damaging |
0.99 |
|
PIT4576001:Prdm1
|
UTSW |
10 |
44,334,504 (GRCm39) |
start codon destroyed |
probably null |
0.05 |
|
R0008:Prdm1
|
UTSW |
10 |
44,317,675 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0166:Prdm1
|
UTSW |
10 |
44,316,087 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0226:Prdm1
|
UTSW |
10 |
44,332,692 (GRCm39) |
missense |
probably benign |
0.03 |
|
R0284:Prdm1
|
UTSW |
10 |
44,332,622 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0398:Prdm1
|
UTSW |
10 |
44,315,805 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1200:Prdm1
|
UTSW |
10 |
44,326,126 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1405:Prdm1
|
UTSW |
10 |
44,315,961 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1405:Prdm1
|
UTSW |
10 |
44,315,961 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1438:Prdm1
|
UTSW |
10 |
44,318,124 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1519:Prdm1
|
UTSW |
10 |
44,315,982 (GRCm39) |
nonsense |
probably null |
|
|
R1886:Prdm1
|
UTSW |
10 |
44,315,754 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R2070:Prdm1
|
UTSW |
10 |
44,317,408 (GRCm39) |
missense |
possibly damaging |
0.82 |
|
R2508:Prdm1
|
UTSW |
10 |
44,322,803 (GRCm39) |
missense |
probably benign |
0.37 |
|
R3087:Prdm1
|
UTSW |
10 |
44,322,823 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3150:Prdm1
|
UTSW |
10 |
44,334,488 (GRCm39) |
splice site |
probably null |
|
|
R4490:Prdm1
|
UTSW |
10 |
44,322,903 (GRCm39) |
nonsense |
probably null |
|
|
R4647:Prdm1
|
UTSW |
10 |
44,315,686 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4911:Prdm1
|
UTSW |
10 |
44,318,048 (GRCm39) |
missense |
possibly damaging |
0.90 |
|
R4925:Prdm1
|
UTSW |
10 |
44,316,165 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5153:Prdm1
|
UTSW |
10 |
44,326,221 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R5247:Prdm1
|
UTSW |
10 |
44,316,098 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5792:Prdm1
|
UTSW |
10 |
44,326,224 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6164:Prdm1
|
UTSW |
10 |
44,326,191 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6247:Prdm1
|
UTSW |
10 |
44,322,782 (GRCm39) |
splice site |
probably null |
|
|
R7196:Prdm1
|
UTSW |
10 |
44,332,988 (GRCm39) |
missense |
probably benign |
0.14 |
|
R7270:Prdm1
|
UTSW |
10 |
44,317,566 (GRCm39) |
missense |
probably benign |
0.07 |
|
R7384:Prdm1
|
UTSW |
10 |
44,334,503 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7822:Prdm1
|
UTSW |
10 |
44,334,478 (GRCm39) |
missense |
probably benign |
0.01 |
|
R8809:Prdm1
|
UTSW |
10 |
44,315,749 (GRCm39) |
missense |
probably benign |
|
|
R8827:Prdm1
|
UTSW |
10 |
44,334,476 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8932:Prdm1
|
UTSW |
10 |
44,317,335 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8958:Prdm1
|
UTSW |
10 |
44,316,729 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9009:Prdm1
|
UTSW |
10 |
44,322,997 (GRCm39) |
missense |
probably benign |
0.02 |
|
R9020:Prdm1
|
UTSW |
10 |
44,316,036 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9176:Prdm1
|
UTSW |
10 |
44,316,123 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9378:Prdm1
|
UTSW |
10 |
44,316,150 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9471:Prdm1
|
UTSW |
10 |
44,326,174 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9535:Prdm1
|
UTSW |
10 |
44,317,608 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9554:Prdm1
|
UTSW |
10 |
44,317,242 (GRCm39) |
missense |
probably benign |
0.01 |
|
Z1088:Prdm1
|
UTSW |
10 |
44,317,921 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Z1176:Prdm1
|
UTSW |
10 |
44,322,829 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- GATAAGCACCTCTTTGGGGTG -3'
(R):5'- CAGAGCCTTAAGAGCTCCAG -3'
Sequencing Primer
(F):5'- ACCTCTTTGGGGTGCTCCG -3'
(R):5'- GAAACACGGTGTCACCCCTG -3'
|
| Posted On |
2015-06-12 |
Incidental Mutation