Incidental Mutation 'R3150:Prdm1'
ID 271635
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 040602-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R3150 (G1)
Quality Score 225
Status Not validated
Chromosome 10
Chromosomal Location 44313173-44404497 bp(-) (GRCm39)
Type of Mutation splice site
DNA Base Change (assembly) A to T at 44334488 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000151237 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000039174] [ENSMUST00000105490] [ENSMUST00000218369]
AlphaFold Q60636
Predicted Effect probably benign
Transcript: ENSMUST00000039174
AA Change: W13R

PolyPhen 2 Score 0.042 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000039248
Gene: ENSMUSG00000038151
AA Change: W13R

DomainStartEndE-ValueType
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 null
Transcript: ENSMUST00000105490
AA Change: L6*
SMART Domains Protein: ENSMUSP00000101129
Gene: ENSMUSG00000038151
AA Change: L6*

DomainStartEndE-ValueType
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 noncoding transcript
Transcript: ENSMUST00000167340
Predicted Effect probably null
Transcript: ENSMUST00000218369
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.1%
Validation Efficiency
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: 42 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Akna A T 4: 63,313,590 (GRCm39) S178T possibly damaging Het
Cabin1 A G 10: 75,492,745 (GRCm39) L1850P probably damaging Het
Ccdc178 G T 18: 22,200,709 (GRCm39) A416E possibly damaging Het
Ces1g C T 8: 94,052,444 (GRCm39) V282I probably benign Het
Col4a3 T G 1: 82,634,858 (GRCm39) probably null Het
Crat C T 2: 30,303,871 (GRCm39) probably null Het
Csf2ra C A 19: 61,215,758 (GRCm39) A16S possibly damaging Het
Cspg4b A T 13: 113,488,294 (GRCm39) Q105H probably damaging Het
Cyp4f18 T C 8: 72,747,044 (GRCm39) D317G possibly damaging Het
Ddb1 T A 19: 10,590,346 (GRCm39) M291K probably benign Het
Fcgbpl1 C A 7: 27,853,620 (GRCm39) T1528N probably benign Het
Gfod2 C T 8: 106,443,853 (GRCm39) G230D probably benign Het
Git2 A G 5: 114,868,410 (GRCm39) S257P probably damaging Het
Gm5592 A G 7: 40,937,804 (GRCm39) E362G probably benign Het
Gpatch2l A G 12: 86,291,089 (GRCm39) T91A possibly damaging Het
Hjurp A G 1: 88,194,283 (GRCm39) probably benign Het
Hnrnph1 T A 11: 50,276,619 (GRCm39) V439E probably benign Het
Itgad C A 7: 127,790,153 (GRCm39) H651N possibly damaging Het
Map3k20 C T 2: 72,202,336 (GRCm39) T189M probably damaging Het
Mapk11 T C 15: 89,029,653 (GRCm39) probably null Het
Mrc2 G A 11: 105,239,257 (GRCm39) probably null Het
Nmral1 G A 16: 4,534,333 (GRCm39) T36I probably damaging Het
Or4c1 C T 2: 89,133,562 (GRCm39) V125M possibly damaging Het
Or5b119 A G 19: 13,456,824 (GRCm39) V246A probably damaging Het
Or7e169 A G 9: 19,757,510 (GRCm39) I135T possibly damaging Het
Padi6 A G 4: 140,462,700 (GRCm39) L307P probably damaging Het
Pkd1 G T 17: 24,798,765 (GRCm39) R2691L probably benign Het
Ppp2r2a G A 14: 67,261,214 (GRCm39) R169W probably damaging Het
Robo1 C T 16: 72,767,157 (GRCm39) P443L possibly damaging Het
Rtn4 CGAGGAGGAGGAGGAGGA CGAGGAGGAGGAGGA 11: 29,643,308 (GRCm39) probably benign Het
Shprh A G 10: 11,045,774 (GRCm39) H865R probably damaging Het
Spats1 A T 17: 45,775,480 (GRCm39) S15T probably damaging Het
Srgap2 T C 1: 131,220,327 (GRCm39) T216A probably benign Het
Sry ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG ACTGCTGCTGCTGCTGCTGCTGCTGCTGCTG Y: 2,662,944 (GRCm39) probably benign Het
Tie1 G A 4: 118,333,022 (GRCm39) A902V probably damaging Het
Usp22 T C 11: 61,051,407 (GRCm39) Q312R probably damaging Het
Vmn2r32 T C 7: 7,475,554 (GRCm39) Y443C probably benign Het
Vps13d A C 4: 144,813,360 (GRCm39) D3274E probably damaging Het
Wdr62 A T 7: 29,971,095 (GRCm39) N167K possibly damaging Het
Xpo5 A G 17: 46,553,173 (GRCm39) probably null Het
Zswim7 A T 11: 62,164,611 (GRCm39) I43N possibly damaging Het
Zswim9 T C 7: 13,011,196 (GRCm39) T51A possibly damaging Het
Other mutations in Prdm1
AlleleSourceChrCoordTypePredicted EffectPPH 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
R4165:Prdm1 UTSW 10 44,317,572 (GRCm39) missense probably benign 0.11
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'- AGCGCTGGTTTCTACTGAGG -3'
(R):5'- TTGGTAAAGAAGTCTGCGGC -3'

Sequencing Primer
(F):5'- GCTGGTTTCTACTGAGGCTTCATTC -3'
(R):5'- AAGAGTAGTCAGTCGCTCGCTC -3'
Posted On 2015-03-25