Incidental Mutation 'R9176:Prdm1'
ID 696689
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
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R9176 (G1)
Quality Score 225.009
Status Validated
Chromosome 10
Chromosomal Location 44313173-44404497 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 44316123 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Arginine at position 671 (H671R)
Ref Sequence ENSEMBL: ENSMUSP00000101129 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000039174] [ENSMUST00000105490] [ENSMUST00000218369]
AlphaFold Q60636
Predicted Effect probably damaging
Transcript: ENSMUST00000039174
AA Change: H704R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000039248
Gene: ENSMUSG00000038151
AA Change: H704R

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 damaging
Transcript: ENSMUST00000105490
AA Change: H671R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000101129
Gene: ENSMUSG00000038151
AA Change: H671R

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 probably damaging
Transcript: ENSMUST00000218369
AA Change: H686R

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 98.9%
Validation Efficiency 100% (70/70)
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: 70 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700001J03Rik T C 5: 146,121,004 (GRCm39) D119G probably damaging Het
1700123K08Rik T C 5: 138,561,155 (GRCm39) D169G probably damaging Het
Abcd2 T G 15: 91,075,623 (GRCm39) R63S probably benign Het
Ankrd55 T C 13: 112,459,610 (GRCm39) V68A possibly damaging Het
Avil T C 10: 126,852,248 (GRCm39) Y678H probably damaging Het
Bltp1 T A 3: 37,010,852 (GRCm39) V1750E possibly damaging Het
Cd300ld2 C A 11: 114,904,772 (GRCm39) E32* probably null Het
Chuk A T 19: 44,076,442 (GRCm39) L423Q probably damaging Het
Cisd3 A G 11: 97,579,127 (GRCm39) T90A probably damaging Het
Cmpk2 T A 12: 26,524,027 (GRCm39) S275T probably benign Het
Cntnap5c T A 17: 58,620,730 (GRCm39) N936K probably damaging Het
Col15a1 G C 4: 47,288,200 (GRCm39) probably benign Het
Col4a4 G T 1: 82,463,349 (GRCm39) P1047Q unknown Het
Col6a4 A G 9: 105,938,755 (GRCm39) L1321P probably damaging Het
Crat A G 2: 30,297,892 (GRCm39) F211L probably damaging Het
Csmd3 T C 15: 47,864,937 (GRCm39) Q27R Het
Dapk1 T C 13: 60,866,262 (GRCm39) V205A probably damaging Het
Ddx20 T C 3: 105,586,158 (GRCm39) N729S probably benign Het
Derl2 A G 11: 70,904,376 (GRCm39) V139A possibly damaging Het
Dscam C T 16: 96,486,553 (GRCm39) D1041N probably benign Het
Fbxo2 A T 4: 148,250,147 (GRCm39) R226W probably damaging Het
Fhip1b A C 7: 105,030,585 (GRCm39) H180Q probably benign Het
Fhip2b T C 14: 70,826,540 (GRCm39) K183E probably benign Het
Gpr19 A G 6: 134,846,718 (GRCm39) S322P probably damaging Het
Gvin2 T C 7: 105,551,262 (GRCm39) K597E possibly damaging Het
Herc6 A G 6: 57,636,663 (GRCm39) N793S probably benign Het
Ikbke A T 1: 131,191,025 (GRCm39) S563T probably benign Het
Il1r2 T C 1: 40,144,478 (GRCm39) L55P probably damaging Het
Klhl8 C A 5: 104,012,111 (GRCm39) A575S probably benign Het
Lims1 T G 10: 58,254,265 (GRCm39) C340G probably damaging Het
Loxl3 G A 6: 83,026,292 (GRCm39) C460Y probably damaging Het
Mapk9 T A 11: 49,763,565 (GRCm39) L152* probably null Het
Mef2d T C 3: 88,066,463 (GRCm39) V144A possibly damaging Het
Mertk A G 2: 128,620,892 (GRCm39) D578G possibly damaging Het
Mettl1 C A 10: 126,881,250 (GRCm39) Q254K probably benign Het
Naip2 T C 13: 100,298,707 (GRCm39) E443G probably damaging Het
Ndor1 A G 2: 25,138,241 (GRCm39) F484L probably damaging Het
Neurl1b C T 17: 26,660,055 (GRCm39) T425I possibly damaging Het
Nomo1 G A 7: 45,730,828 (GRCm39) V1104M possibly damaging Het
Or13a19 G T 7: 139,903,121 (GRCm39) G170C probably damaging Het
Or13p8 T A 4: 118,583,850 (GRCm39) Y135* probably null Het
Or4c10b T C 2: 89,711,515 (GRCm39) V115A probably benign Het
Or5b95 A G 19: 12,657,600 (GRCm39) M43V probably benign Het
Or5p57 A G 7: 107,665,246 (GRCm39) V223A probably benign Het
Or8g20 T A 9: 39,396,247 (GRCm39) M98L probably benign Het
Or9i2 A G 19: 13,815,796 (GRCm39) V247A probably damaging Het
Parp4 A G 14: 56,873,274 (GRCm39) K1173E possibly damaging Het
Phkb T A 8: 86,697,623 (GRCm39) N477K probably damaging Het
Plekha7 T G 7: 115,739,926 (GRCm39) I812L possibly damaging Het
Plxnb1 A G 9: 108,941,651 (GRCm39) T1711A probably damaging Het
Polg A G 7: 79,109,857 (GRCm39) V382A probably benign Het
Pomt2 T A 12: 87,194,451 (GRCm39) probably benign Het
Prkca G A 11: 107,870,244 (GRCm39) R15C possibly damaging Het
Prkch T A 12: 73,746,968 (GRCm39) N282K probably damaging Het
Ptpn6 T C 6: 124,702,249 (GRCm39) R385G probably benign Het
Rad21 A T 15: 51,841,455 (GRCm39) M87K probably damaging Het
Safb2 ACTTCTTCT ACTTCT 17: 56,878,292 (GRCm39) probably benign Het
Scn1a A T 2: 66,103,689 (GRCm39) V1857E probably damaging Het
Shprh A G 10: 11,036,320 (GRCm39) T386A probably benign Het
Slco1b2 T C 6: 141,598,229 (GRCm39) L94P probably damaging Het
Snx29 A G 16: 11,236,728 (GRCm39) N90D probably benign Het
Stt3a A T 9: 36,662,592 (GRCm39) H222Q probably damaging Het
Tbc1d5 T C 17: 51,089,363 (GRCm39) T584A probably benign Het
Tktl2 T C 8: 66,964,664 (GRCm39) V74A probably damaging Het
Tpp2 A G 1: 44,031,553 (GRCm39) N1124D probably null Het
Trpv1 A T 11: 73,130,481 (GRCm39) T196S probably benign Het
Ulk4 T C 9: 120,974,128 (GRCm39) E968G probably benign Het
Zbtb8a G T 4: 129,254,221 (GRCm39) T91K probably damaging Het
Zfp317 T A 9: 19,559,163 (GRCm39) V459E probably damaging Het
Zfp790 A G 7: 29,529,387 (GRCm39) T691A probably benign 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
R3150:Prdm1 UTSW 10 44,334,488 (GRCm39) splice site probably null
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
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'- TCGCTGATGTCGAACCTCTC -3'
(R):5'- CTCCCGAGGTTTCTGGCTATTG -3'

Sequencing Primer
(F):5'- CAATTTCTTCATTGATTCGGGTCAG -3'
(R):5'- GCTGCAAACAATTAATCTGGTCTTCC -3'
Posted On 2022-02-07