Incidental Mutation 'R6753:Prdm9'
ID 530930
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 044870-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.351) question?
Stock # R6753 (G1)
Quality Score 225.009
Status Validated
Chromosome 17
Chromosomal Location 15763341-15784616 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 15765218 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Asparagine at position 521 (Y521N)
Ref Sequence ENSEMBL: ENSMUSP00000131871 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000167994]
AlphaFold Q96EQ9
Predicted Effect noncoding transcript
Transcript: ENSMUST00000128267
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130297
Predicted Effect probably benign
Transcript: ENSMUST00000167994
AA Change: Y521N

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000131871
Gene: ENSMUSG00000051977
AA Change: Y521N

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: ENSMUST00000231919
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.3%
  • 20x: 95.1%
Validation Efficiency 99% (68/69)
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: 64 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aatk G A 11: 119,900,977 (GRCm39) P1083S probably benign Het
Abcb5 T A 12: 118,908,641 (GRCm39) N101I possibly damaging Het
Adrb2 A G 18: 62,312,624 (GRCm39) V67A possibly damaging Het
Agk T A 6: 40,345,504 (GRCm39) probably null Het
Akap10 A T 11: 61,777,603 (GRCm39) M586K probably damaging Het
Akt3 A T 1: 176,877,756 (GRCm39) Y337* probably null Het
Armc1 A G 3: 19,198,562 (GRCm39) F133L possibly damaging Het
Bank1 T C 3: 135,799,069 (GRCm39) E424G probably damaging Het
Cacna1a A G 8: 85,306,834 (GRCm39) E1363G probably damaging Het
Cacna1d C A 14: 29,764,743 (GRCm39) A2076S probably damaging Het
Ccdc73 T A 2: 104,821,869 (GRCm39) L606* probably null Het
Ccdc8 C T 7: 16,730,562 (GRCm39) Q684* probably null Het
Ces1b T A 8: 93,793,648 (GRCm39) K314* probably null Het
Ces1e T A 8: 93,941,756 (GRCm39) N238I probably damaging Het
Chd4 A G 6: 125,091,263 (GRCm39) N1238S probably benign Het
Cmtr2 T A 8: 110,949,611 (GRCm39) D640E probably damaging Het
Col7a1 C T 9: 108,787,196 (GRCm39) T559I unknown Het
Comt T C 16: 18,226,771 (GRCm39) K205R probably benign Het
Dbp A T 7: 45,357,828 (GRCm39) E232V probably damaging Het
Dcbld2 A G 16: 58,276,493 (GRCm39) T470A possibly damaging Het
Eml6 T A 11: 29,704,987 (GRCm39) D1519V probably damaging Het
Evpl T A 11: 116,128,732 (GRCm39) H31L possibly damaging Het
Exoc1 T A 5: 76,711,186 (GRCm39) I86N probably damaging Het
Fat3 C T 9: 15,826,357 (GRCm39) E4532K possibly damaging Het
Fgfr3 T C 5: 33,889,503 (GRCm39) S301P probably benign Het
Gas2l1 C T 11: 5,014,254 (GRCm39) V69I probably damaging Het
Gm2042 T A 12: 87,924,854 (GRCm39) I107K probably damaging Het
Gucy1b1 T C 3: 81,947,054 (GRCm39) D385G probably null Het
Ints1 T A 5: 139,750,930 (GRCm39) E824D probably damaging Het
Itfg1 T C 8: 86,561,707 (GRCm39) D142G probably benign Het
Jaml A G 9: 45,018,677 (GRCm39) N359D probably benign Het
Kcnh7 T A 2: 62,680,721 (GRCm39) I289L probably benign Het
Klf12 G A 14: 100,347,212 (GRCm39) Q40* probably null Het
Mcm4 A C 16: 15,447,226 (GRCm39) N579K possibly damaging Het
Mfsd2b A T 12: 4,917,358 (GRCm39) F179I possibly damaging Het
Mmp11 C T 10: 75,764,208 (GRCm39) V86M probably damaging Het
Mogs T C 6: 83,092,863 (GRCm39) V101A probably damaging Het
Narf T A 11: 121,133,452 (GRCm39) H84Q probably benign Het
Or5ak4 C A 2: 85,162,142 (GRCm39) M33I probably benign Het
Otog A C 7: 45,898,495 (GRCm39) E204D probably benign Het
Parp8 G A 13: 117,031,651 (GRCm39) H354Y possibly damaging Het
Pcnx1 C A 12: 82,011,254 (GRCm39) D1238E probably damaging Het
Pi4ka A G 16: 17,194,846 (GRCm39) L184P possibly damaging Het
Pkd1l3 C T 8: 110,351,081 (GRCm39) T642I probably damaging Het
Pkhd1l1 G A 15: 44,453,059 (GRCm39) E3995K probably benign Het
Prex2 A G 1: 11,254,680 (GRCm39) S1105G probably damaging Het
Prss35 T A 9: 86,638,153 (GRCm39) F308I probably damaging Het
Rab22a C T 2: 173,542,848 (GRCm39) A167V probably benign Het
Rims2 A G 15: 39,430,369 (GRCm39) Q871R possibly damaging Het
Rorb A T 19: 18,934,611 (GRCm39) M253K probably benign Het
Ryr3 T C 2: 112,482,955 (GRCm39) D4269G probably damaging Het
Snx11 T C 11: 96,660,732 (GRCm39) probably benign Het
Son A G 16: 91,454,076 (GRCm39) Q941R probably damaging Het
Sptbn2 G T 19: 4,797,813 (GRCm39) R1880L probably benign Het
Sun1 G A 5: 139,201,014 (GRCm39) probably null Het
Tprn A G 2: 25,154,050 (GRCm39) R451G probably benign Het
Trbv30 T A 6: 41,258,311 (GRCm39) M1K probably null Het
Ttn C A 2: 76,568,565 (GRCm39) G25697W probably damaging Het
Ubb T G 11: 62,442,353 (GRCm39) probably null Het
Unc13b C T 4: 43,239,331 (GRCm39) R1038C probably damaging Het
Usp7 T C 16: 8,514,775 (GRCm39) M687V probably benign Het
Zfp160 G A 17: 21,240,996 (GRCm39) M21I probably benign Het
Zfp868 T C 8: 70,064,747 (GRCm39) N196S probably benign Het
Zup1 A T 10: 33,804,025 (GRCm39) I483N 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
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'- CCCTGCAAACATAGGGCTTC -3'
(R):5'- AGGCAGAGGATTTCAACAACC -3'

Sequencing Primer
(F):5'- AGGTCTGACTTCTGTGTAAAGCCC -3'
(R):5'- GGCAGAGGATTTCAACAACCTTTCC -3'
Posted On 2018-08-01