Incidental Mutation 'R7575:Prdm9'
ID 586379
Institutional Source Beutler Lab
Gene Symbol Prdm9
Ensembl Gene ENSMUSG00000051977
Gene Name PR domain containing 9
Synonyms Meisetz, repro7, Dsbc1, Rcr1, G1-419-29
MMRRC Submission 045632-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.351) question?
Stock # R7575 (G1)
Quality Score 201.009
Status Not validated
Chromosome 17
Chromosomal Location 15763341-15784616 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 15764890 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Cysteine to Tyrosine at position 630 (C630Y)
Ref Sequence ENSEMBL: ENSMUSP00000131871 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000167994]
AlphaFold Q96EQ9
Predicted Effect probably damaging
Transcript: ENSMUST00000167994
AA Change: C630Y

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000131871
Gene: ENSMUSG00000051977
AA Change: C630Y

DomainStartEndE-ValueType
KRAB 30 89 5.54e-8 SMART
Pfam:SSXRD 175 205 1.5e-20 PFAM
SET 248 368 2.56e-2 SMART
ZnF_C2H2 392 415 3.29e-1 SMART
ZnF_C2H2 516 535 4.74e1 SMART
ZnF_C2H2 541 563 9.73e-4 SMART
ZnF_C2H2 569 591 1.3e-4 SMART
ZnF_C2H2 597 619 1.3e-4 SMART
ZnF_C2H2 625 647 4.24e-4 SMART
ZnF_C2H2 653 675 4.24e-4 SMART
ZnF_C2H2 681 703 1.95e-3 SMART
ZnF_C2H2 709 731 5.99e-4 SMART
ZnF_C2H2 737 759 1.95e-3 SMART
ZnF_C2H2 765 787 1.95e-3 SMART
ZnF_C2H2 793 815 1.3e-4 SMART
ZnF_C2H2 821 843 1.6e-4 SMART
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.0%
Validation Efficiency
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 zinc finger protein with histone methyltransferase activity that catalyzes histone H3 lysine 4 trimethylation (H3K4me3) during meiotic prophase. This protein contains multiple domains, including a Kruppel-associated box (KRAB) domain, an SSX repression domain (SSXRD), a PRD1-BF1 and RIZ homologous region, a subclass of SET (PR/SET) domain, and a tandem array of C2H2 zinc fingers. The zinc finger array recognizes a short sequence motif, leading to local H3K4me3, and meiotic recombination hotspot activity. The observed allelic variation alters the DNA-binding sequence specificity of the protein, resulting in distinct meiotic recombination hotspots amongst individuals and populations. Multiple alternate alleles of this gene have been described. [provided by RefSeq, Jul 2015]
PHENOTYPE: Mice homozygous for a knock-out allele show decreased oocyte number, azoospermia, and sterility in both sexes due to severe impairment of the double-stranded break repair pathway, deficient pairing of homologous chromosomes, and impaired sex body formation. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 91 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
3425401B19Rik C T 14: 32,384,589 (GRCm39) V459I probably benign Het
4921539E11Rik T C 4: 103,088,192 (GRCm39) D439G probably damaging Het
Adam18 T C 8: 25,115,873 (GRCm39) N607S possibly damaging Het
Adamtsl3 A T 7: 82,223,756 (GRCm39) N1179I possibly damaging Het
Adarb1 A G 10: 77,139,129 (GRCm39) F552S probably damaging Het
Ago1 T C 4: 126,347,701 (GRCm39) E394G probably benign Het
Alb G A 5: 90,613,788 (GRCm39) C224Y probably damaging Het
Alms1 T A 6: 85,599,141 (GRCm39) H1322Q possibly damaging Het
Arhgef18 T G 8: 3,501,635 (GRCm39) V643G probably damaging Het
Asah2 T C 19: 31,994,103 (GRCm39) Q414R probably benign Het
Atpsckmt C T 15: 31,606,186 (GRCm39) A48V probably damaging Het
Bbc3 G A 7: 16,046,292 (GRCm39) R76H possibly damaging Het
Bub1b T A 2: 118,471,639 (GRCm39) S1000T possibly damaging Het
Bud23 A T 5: 135,089,982 (GRCm39) Y70* probably null Het
C1d A G 11: 17,212,694 (GRCm39) E13G probably damaging Het
Camk1 T A 6: 113,315,325 (GRCm39) I158F probably damaging Het
Ccr2 A C 9: 123,905,843 (GRCm39) D41A probably benign Het
Cdh18 G T 15: 23,400,683 (GRCm39) E348* probably null Het
Col6a3 A G 1: 90,738,321 (GRCm39) L1066P possibly damaging Het
Cyp11b1 T A 15: 74,711,162 (GRCm39) D172V probably benign Het
Cyp2j8 A G 4: 96,358,785 (GRCm39) I378T possibly damaging Het
Cys1 T A 12: 24,718,647 (GRCm39) K69* probably null Het
Dip2c A G 13: 9,678,048 (GRCm39) K1165E probably damaging Het
Drd3 A T 16: 43,637,496 (GRCm39) I232F probably benign Het
Dusp7 T C 9: 106,250,876 (GRCm39) C334R probably damaging Het
Eppk1 A G 15: 75,995,442 (GRCm39) S480P not run Het
Erc1 G T 6: 119,801,721 (GRCm39) P99T possibly damaging Het
Fam170b C T 14: 32,558,155 (GRCm39) P330L unknown Het
Fasn G T 11: 120,703,513 (GRCm39) T1573K possibly damaging Het
Fras1 A T 5: 96,691,173 (GRCm39) T130S probably benign Het
Fzd4 A G 7: 89,056,918 (GRCm39) I322V possibly damaging Het
Gbp10 G A 5: 105,384,015 (GRCm39) probably benign Het
Gdpd4 A T 7: 97,647,448 (GRCm39) H365L probably benign Het
Gfy A G 7: 44,827,524 (GRCm39) S191P probably benign Het
Ghr A T 15: 3,349,994 (GRCm39) S395T probably damaging Het
Git2 C T 5: 114,904,550 (GRCm39) R123H probably damaging Het
Htt A G 5: 35,062,987 (GRCm39) D2873G probably damaging Het
Idua A T 5: 108,829,565 (GRCm39) D476V probably damaging Het
Inppl1 G A 7: 101,477,689 (GRCm39) R683W probably damaging Het
Ipp T C 4: 116,389,841 (GRCm39) S466P probably benign Het
Iqgap2 A G 13: 95,798,131 (GRCm39) V1058A probably damaging Het
Jmy A T 13: 93,601,103 (GRCm39) Y434* probably null Het
Kmt2d CTGCTGCTG CTGCTGCTGATGCTGCTG 15: 98,747,492 (GRCm39) probably benign Het
Mogs T G 6: 83,092,816 (GRCm39) S85R probably damaging Het
Mroh2b A T 15: 4,964,087 (GRCm39) D863V probably damaging Het
Mtmr10 A T 7: 63,947,213 (GRCm39) I43F probably damaging Het
Mtr T C 13: 12,213,963 (GRCm39) D903G probably benign Het
Ncor1 A G 11: 62,274,082 (GRCm39) V186A probably benign Het
Notch3 C T 17: 32,373,793 (GRCm39) D472N possibly damaging Het
Or4k44 A T 2: 111,368,597 (GRCm39) F12L probably damaging Het
Or6c68 T C 10: 129,157,728 (GRCm39) F79L probably damaging Het
Or8j3c A G 2: 86,253,582 (GRCm39) F146S probably benign Het
Or9i1 T C 19: 13,839,381 (GRCm39) S75P probably damaging Het
Oxr1 T G 15: 41,686,758 (GRCm39) L547V possibly damaging Het
Pappa2 A T 1: 158,642,100 (GRCm39) C1319S probably damaging Het
Papss1 A C 3: 131,348,857 (GRCm39) K623N probably damaging Het
Parp4 T C 14: 56,875,375 (GRCm39) F1198S probably benign Het
Pcare T A 17: 72,057,850 (GRCm39) Q609L probably damaging Het
Pcnt A T 10: 76,225,086 (GRCm39) V1806D probably benign Het
Pitx2 A T 3: 129,009,375 (GRCm39) H98L probably damaging Het
Polq C A 16: 36,911,496 (GRCm39) D2410E probably benign Het
Preb A T 5: 31,115,839 (GRCm39) D201E probably damaging Het
Rasa3 A T 8: 13,645,887 (GRCm39) I151N possibly damaging Het
Rasgrp2 T A 19: 6,454,397 (GRCm39) S147T probably damaging Het
Rev3l A G 10: 39,697,441 (GRCm39) D646G possibly damaging Het
Sdc1 A G 12: 8,840,619 (GRCm39) E128G probably damaging Het
Slamf7 A C 1: 171,466,762 (GRCm39) C148G probably damaging Het
Slc19a2 T C 1: 164,084,691 (GRCm39) S194P probably damaging Het
Spata31 C T 13: 65,070,726 (GRCm39) P958L unknown Het
Sprr2b CTGAGCCTTGTCCTCCTCCAAAGTGCCCTGAGCCTTGTCCTCCCCCAGTATGCTGTGAGCCTTGTCCTCCTCCAAAGTGCCCTGAGCCTTGTCCTCCCCCAGTATGCTGTGAGCCTTGTCCTCC CTGAGCCTTGTCCTCCTCCAAAGTGCCCTGAGCCTTGTCCTCCCCCAGTATGCTGTGAGCCTTGTCCTCC 3: 92,224,826 (GRCm39) probably benign Het
Stradb A G 1: 59,027,739 (GRCm39) I90V probably benign Het
Tas2r134 A G 2: 51,518,166 (GRCm39) D215G probably damaging Het
Tbc1d4 T C 14: 101,685,025 (GRCm39) K1209E probably damaging Het
Thbs1 A G 2: 117,953,409 (GRCm39) D942G probably damaging Het
Tmem107 C T 11: 68,963,633 (GRCm39) P139S probably benign Het
Tmem216 A T 19: 10,529,266 (GRCm39) M40K probably benign Het
Tpte A G 8: 22,845,498 (GRCm39) Y516C probably damaging Het
Trim54 G A 5: 31,291,431 (GRCm39) G184D possibly damaging Het
Try5 A T 6: 41,288,748 (GRCm39) L157Q probably benign Het
Ubqlnl G A 7: 103,797,697 (GRCm39) A600V probably damaging Het
Uhrf2 C A 19: 30,048,768 (GRCm39) P258Q probably damaging Het
Ush2a A T 1: 188,554,885 (GRCm39) E3554D possibly damaging Het
Usp40 A C 1: 87,877,682 (GRCm39) L1158W probably damaging Het
Vmn1r121 T A 7: 20,832,198 (GRCm39) R81* probably null Het
Vmn1r203 C A 13: 22,708,588 (GRCm39) T123K probably benign Het
Vmn2r101 T C 17: 19,831,654 (GRCm39) V550A probably benign Het
Wdr49 A T 3: 75,358,193 (GRCm39) M184K probably damaging Het
Wipi2 A G 5: 142,643,987 (GRCm39) N123S probably damaging Het
Zbtb14 T C 17: 69,694,442 (GRCm39) F47L probably damaging Het
Zc3h7b C A 15: 81,662,086 (GRCm39) S385* probably null Het
Zhx2 T A 15: 57,686,658 (GRCm39) F676I probably damaging Het
Other mutations in Prdm9
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01302:Prdm9 APN 17 15,773,608 (GRCm39) missense probably benign 0.11
IGL02322:Prdm9 APN 17 15,783,110 (GRCm39) missense probably damaging 0.99
IGL02354:Prdm9 APN 17 15,783,109 (GRCm39) missense probably damaging 1.00
IGL02361:Prdm9 APN 17 15,783,109 (GRCm39) missense probably damaging 1.00
IGL02724:Prdm9 APN 17 15,783,522 (GRCm39) missense probably benign 0.07
IGL03120:Prdm9 APN 17 15,765,193 (GRCm39) missense probably benign
berlin UTSW 17 15,782,702 (GRCm39) missense probably damaging 0.96
R0173:Prdm9 UTSW 17 15,764,297 (GRCm39) missense probably benign 0.00
R0173:Prdm9 UTSW 17 15,764,275 (GRCm39) missense probably benign 0.02
R0309:Prdm9 UTSW 17 15,777,646 (GRCm39) missense probably damaging 0.98
R1420:Prdm9 UTSW 17 15,764,638 (GRCm39) missense probably damaging 1.00
R3498:Prdm9 UTSW 17 15,783,207 (GRCm39) splice site probably benign
R3714:Prdm9 UTSW 17 15,777,623 (GRCm39) nonsense probably null
R4118:Prdm9 UTSW 17 15,764,275 (GRCm39) missense probably benign 0.02
R4369:Prdm9 UTSW 17 15,764,708 (GRCm39) missense probably benign 0.14
R4691:Prdm9 UTSW 17 15,773,640 (GRCm39) missense probably benign 0.03
R4742:Prdm9 UTSW 17 15,773,783 (GRCm39) missense probably damaging 0.99
R4910:Prdm9 UTSW 17 15,764,585 (GRCm39) missense probably benign 0.08
R5056:Prdm9 UTSW 17 15,782,679 (GRCm39) missense possibly damaging 0.93
R5130:Prdm9 UTSW 17 15,764,729 (GRCm39) missense probably benign 0.00
R5175:Prdm9 UTSW 17 15,777,713 (GRCm39) missense probably benign 0.04
R5187:Prdm9 UTSW 17 15,783,155 (GRCm39) missense probably damaging 0.98
R5213:Prdm9 UTSW 17 15,775,416 (GRCm39) missense probably damaging 0.98
R5270:Prdm9 UTSW 17 15,773,625 (GRCm39) missense probably benign 0.16
R5635:Prdm9 UTSW 17 15,782,702 (GRCm39) missense probably damaging 0.96
R6753:Prdm9 UTSW 17 15,765,218 (GRCm39) missense probably benign 0.00
R6857:Prdm9 UTSW 17 15,764,518 (GRCm39) missense probably benign 0.04
R7041:Prdm9 UTSW 17 15,765,257 (GRCm39) missense possibly damaging 0.56
R7355:Prdm9 UTSW 17 15,765,497 (GRCm39) missense probably benign 0.01
R7410:Prdm9 UTSW 17 15,765,259 (GRCm39) missense possibly damaging 0.73
R7570:Prdm9 UTSW 17 15,775,914 (GRCm39) missense probably benign 0.14
R7571:Prdm9 UTSW 17 15,783,526 (GRCm39) missense probably damaging 0.98
R7593:Prdm9 UTSW 17 15,764,867 (GRCm39) missense possibly damaging 0.81
R7664:Prdm9 UTSW 17 15,775,833 (GRCm39) missense probably damaging 0.99
R7755:Prdm9 UTSW 17 15,765,226 (GRCm39) missense probably damaging 1.00
R7817:Prdm9 UTSW 17 15,779,311 (GRCm39) missense probably damaging 1.00
R7875:Prdm9 UTSW 17 15,773,804 (GRCm39) nonsense probably null
R8110:Prdm9 UTSW 17 15,774,960 (GRCm39) missense probably damaging 1.00
R8222:Prdm9 UTSW 17 15,765,035 (GRCm39) missense possibly damaging 0.93
R8405:Prdm9 UTSW 17 15,764,456 (GRCm39) missense probably benign 0.22
R8695:Prdm9 UTSW 17 15,765,019 (GRCm39) missense probably damaging 1.00
R8947:Prdm9 UTSW 17 15,764,270 (GRCm39) missense possibly damaging 0.96
X0021:Prdm9 UTSW 17 15,773,734 (GRCm39) nonsense probably null
Predicted Primers PCR Primer
(F):5'- CTGGATGAGGACTGACTTCG -3'
(R):5'- GGAGAAGCCCTATGTTTGCAGG -3'

Sequencing Primer
(F):5'- AGGACTGACTTCGCTGTAAAGCC -3'
(R):5'- AGCCCTATGTTTGCAGGGAGTG -3'
Posted On 2019-10-24