Incidental Mutation 'R5635:Prdm9'
ID 448687
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 043286-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.351) question?
Stock # R5635 (G1)
Quality Score 225
Status Validated
Chromosome 17
Chromosomal Location 15763341-15784616 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to C at 15782702 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glutamic Acid at position 96 (D96E)
Ref Sequence ENSEMBL: ENSMUSP00000131871 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000147532] [ENSMUST00000167994]
AlphaFold Q96EQ9
Predicted Effect noncoding transcript
Transcript: ENSMUST00000132675
Predicted Effect noncoding transcript
Transcript: ENSMUST00000139911
Predicted Effect probably benign
Transcript: ENSMUST00000147532
SMART Domains Protein: ENSMUSP00000118454
Gene: ENSMUSG00000051977

DomainStartEndE-ValueType
Pfam:SSXRD 49 81 1.8e-19 PFAM
SET 123 243 2.56e-2 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000167994
AA Change: D96E

PolyPhen 2 Score 0.964 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000131871
Gene: ENSMUSG00000051977
AA Change: D96E

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
Predicted Effect noncoding transcript
Transcript: ENSMUST00000178455
SMART Domains Protein: ENSMUSP00000137164
Gene: ENSMUSG00000095920

DomainStartEndE-ValueType
Pfam:Ribosomal_S21 11 50 1.4e-13 PFAM
Meta Mutation Damage Score 0.0922 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.8%
  • 10x: 97.6%
  • 20x: 96.0%
Validation Efficiency 99% (90/91)
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: 85 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
9330159F19Rik T A 10: 29,094,273 (GRCm39) M53K possibly damaging Het
Aldh3b3 C T 19: 4,018,512 (GRCm39) T409I probably benign Het
Ankrd13a C A 5: 114,939,778 (GRCm39) H468Q possibly damaging Het
Ap2a1 A C 7: 44,573,325 (GRCm39) probably benign Het
Arfgef1 A T 1: 10,259,085 (GRCm39) S671T possibly damaging Het
C1ra G A 6: 124,493,683 (GRCm39) C145Y probably damaging Het
Catsperd G A 17: 56,939,335 (GRCm39) V55M possibly damaging Het
Ccdc30 T C 4: 119,216,871 (GRCm39) N123D possibly damaging Het
Cdc20 A T 4: 118,293,224 (GRCm39) V232E possibly damaging Het
Cfap251 A T 5: 123,460,635 (GRCm39) Q225L probably benign Het
Cfap58 T A 19: 47,971,981 (GRCm39) V637E possibly damaging Het
Coq4 T A 2: 29,678,367 (GRCm39) V24E possibly damaging Het
Crim1 T A 17: 78,623,070 (GRCm39) F423I probably damaging Het
Crls1 T C 2: 132,706,062 (GRCm39) V262A possibly damaging Het
Crybb1 T C 5: 112,405,425 (GRCm39) probably null Het
Cutc T A 19: 43,744,069 (GRCm39) N23K probably benign Het
Cxcl10 T A 5: 92,495,698 (GRCm39) I82F probably damaging Het
Cyp3a44 A T 5: 145,738,124 (GRCm39) F60L possibly damaging Het
Dhx9 A G 1: 153,359,493 (GRCm39) M35T probably benign Het
Dnah8 A G 17: 30,925,360 (GRCm39) E1265G probably benign Het
Dzank1 C G 2: 144,325,327 (GRCm39) D548H probably damaging Het
Eef2kmt A G 16: 5,066,893 (GRCm39) V120A probably damaging Het
Elp4 A G 2: 105,644,609 (GRCm39) probably null Het
Etl4 A T 2: 20,811,846 (GRCm39) I1310F probably damaging Het
Exoc6b A T 6: 84,828,909 (GRCm39) F492I probably damaging Het
F2rl2 A T 13: 95,837,290 (GRCm39) I112F possibly damaging Het
Farp1 T A 14: 121,513,716 (GRCm39) I837N possibly damaging Het
Fars2 A G 13: 36,594,129 (GRCm39) E378G probably damaging Het
Fgg A G 3: 82,918,730 (GRCm39) T248A probably benign Het
Flrt3 T A 2: 140,502,420 (GRCm39) T403S probably damaging Het
Fndc3b C T 3: 27,596,080 (GRCm39) E170K probably damaging Het
Gm17728 A G 17: 9,641,202 (GRCm39) H104R probably benign Het
H2ac21 C A 3: 96,127,593 (GRCm39) T121K possibly damaging Het
Hivep1 A G 13: 42,313,603 (GRCm39) T1948A probably benign Het
Hspa4l T A 3: 40,700,177 (GRCm39) I23N probably damaging Het
Ighv1-75 A G 12: 115,797,829 (GRCm39) V31A probably benign Het
Kalrn T A 16: 33,834,454 (GRCm39) N627I probably damaging Het
Lrp1b T G 2: 42,542,834 (GRCm39) probably benign Het
Lrrc36 G A 8: 106,184,205 (GRCm39) V480M probably damaging Het
Map4k3 A T 17: 80,920,924 (GRCm39) N534K possibly damaging Het
Mybpc3 C T 2: 90,965,174 (GRCm39) T1081I probably benign Het
Nfrkb T C 9: 31,310,594 (GRCm39) S351P probably damaging Het
Nme4 A T 17: 26,313,205 (GRCm39) V43E probably damaging Het
Notch1 C T 2: 26,366,173 (GRCm39) E794K probably damaging Het
Nufip1 A T 14: 76,363,586 (GRCm39) K270M probably damaging Het
Or10ak16 G T 4: 118,750,832 (GRCm39) G184V probably benign Het
Or1e30 G T 11: 73,678,460 (GRCm39) R232L probably benign Het
Or51b6 G A 7: 103,555,845 (GRCm39) M66I probably benign Het
Or5t5 A G 2: 86,616,070 (GRCm39) probably null Het
Or8g51 A G 9: 38,609,455 (GRCm39) I73T possibly damaging Het
Pcdhb15 T A 18: 37,606,823 (GRCm39) Y18* probably null Het
Pcdhb21 A T 18: 37,646,970 (GRCm39) Y33F probably benign Het
Pds5b T A 5: 150,701,686 (GRCm39) H772Q possibly damaging Het
Pik3r4 C A 9: 105,545,024 (GRCm39) H168N probably benign Het
Pitpnm3 A G 11: 71,957,986 (GRCm39) S386P possibly damaging Het
Plg A G 17: 12,614,641 (GRCm39) H307R probably damaging Het
Prmt8 A G 6: 127,745,692 (GRCm39) S7P probably damaging Het
Prune2 T C 19: 17,095,573 (GRCm39) V359A probably benign Het
Pxn A T 5: 115,689,551 (GRCm39) Q279L probably benign Het
Rarb A T 14: 16,443,788 (GRCm38) C167S probably damaging Het
Rps6kb2 T A 19: 4,211,133 (GRCm39) I131F probably damaging Het
Sec14l3 T A 11: 4,021,484 (GRCm39) V219E probably damaging Het
Simc1 A G 13: 54,673,217 (GRCm39) T522A probably benign Het
Slc1a6 T C 10: 78,624,925 (GRCm39) V110A possibly damaging Het
Slc38a11 T G 2: 65,191,747 (GRCm39) probably null Het
Snx13 T A 12: 35,190,170 (GRCm39) D840E probably benign Het
Sp100 C A 1: 85,609,985 (GRCm39) probably benign Het
Spc24 G T 9: 21,668,686 (GRCm39) L104I probably damaging Het
Surf4 T C 2: 26,823,325 (GRCm39) N4D probably benign Het
Tas2r131 A T 6: 132,934,571 (GRCm39) D79E probably benign Het
Tbc1d20 T C 2: 152,153,381 (GRCm39) S304P probably benign Het
Tbrg1 T C 9: 37,566,287 (GRCm39) probably benign Het
Tmem214 A G 5: 31,028,861 (GRCm39) N150S probably damaging Het
Trappc13 A T 13: 104,286,606 (GRCm39) I217K probably benign Het
Ttc41 T A 10: 86,572,841 (GRCm39) C738S probably benign Het
Ttn T C 2: 76,540,068 (GRCm39) Q25979R probably benign Het
Tubb2b A T 13: 34,312,180 (GRCm39) N204K probably damaging Het
Ube3a T A 7: 58,938,236 (GRCm39) M713K probably damaging Het
Usp37 T C 1: 74,534,970 (GRCm39) probably benign Het
Vegfb T A 19: 6,960,214 (GRCm39) *189C probably null Het
Vmn2r82 A G 10: 79,214,652 (GRCm39) N212D probably benign Het
Vta1 A T 10: 14,543,866 (GRCm39) probably null Het
Xdh T G 17: 74,220,870 (GRCm39) I620L possibly damaging Het
Xpnpep3 A G 15: 81,320,970 (GRCm39) Y283C probably benign Het
Zscan18 A G 7: 12,504,791 (GRCm39) S609P probably benign 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
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
R7575:Prdm9 UTSW 17 15,764,890 (GRCm39) missense probably damaging 1.00
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'- CTGACCCTTGATTCTGAAACACC -3'
(R):5'- TGGTACAGTTCCCAATGGAGAC -3'

Sequencing Primer
(F):5'- CACCCAGTTTTCAGAAGTTGG -3'
(R):5'- AAATGTTAGCACTGGCCCTG -3'
Posted On 2016-12-15