Incidental Mutation 'R3714:Prdm9'
| ID |
259818 |
| 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 |
040707-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.297)
|
| Stock # |
R3714 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
17 |
| Chromosomal Location |
15763341-15784616 bp(-) (GRCm39) |
| Type of Mutation |
nonsense |
| DNA Base Change (assembly) |
T to A
at 15777623 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Lysine to Stop codon
at position 154
(K154*)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000131871
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000147532]
[ENSMUST00000167994]
|
| AlphaFold |
Q96EQ9 |
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000128267
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130297
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000139911
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000147532
AA Change: K29*
|
| SMART Domains |
Protein: ENSMUSP00000118454
Gene: ENSMUSG00000051977
AA Change: K29*
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SSXRD
|
49 |
81 |
1.8e-19 |
PFAM |
|
SET
|
123 |
243 |
2.56e-2 |
SMART |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000167994
AA Change: K154*
|
| SMART Domains |
Protein: ENSMUSP00000131871
Gene: ENSMUSG00000051977
AA Change: K154*
| Domain | Start | End | E-Value | Type |
|---|
|
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: 99.1%
- 3x: 98.5%
- 10x: 97.0%
- 20x: 94.2%
|
| 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: 43 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 9930111J21Rik1 |
T |
C |
11: 48,838,803 (GRCm39) |
T595A |
possibly damaging |
Het |
| Abcd4 |
C |
T |
12: 84,658,533 (GRCm39) |
M223I |
probably benign |
Het |
| Adck5 |
G |
A |
15: 76,478,138 (GRCm39) |
V229I |
probably damaging |
Het |
| Afg2a |
G |
A |
3: 37,487,358 (GRCm39) |
V407I |
probably benign |
Het |
| Ankk1 |
T |
G |
9: 49,333,013 (GRCm39) |
D157A |
possibly damaging |
Het |
| Atp1a2 |
A |
G |
1: 172,106,551 (GRCm39) |
I817T |
probably damaging |
Het |
| Ccdc87 |
A |
G |
19: 4,890,287 (GRCm39) |
S260G |
probably benign |
Het |
| Cers3 |
G |
T |
7: 66,435,823 (GRCm39) |
A261S |
probably benign |
Het |
| Cibar2 |
C |
T |
8: 120,901,576 (GRCm39) |
R43H |
probably damaging |
Het |
| Cntnap5c |
C |
T |
17: 58,199,062 (GRCm39) |
Q119* |
probably null |
Het |
| Cpb2 |
T |
A |
14: 75,520,657 (GRCm39) |
|
probably null |
Het |
| Ddx47 |
T |
A |
6: 134,996,025 (GRCm39) |
I329K |
probably damaging |
Het |
| Elavl3 |
G |
T |
9: 21,929,895 (GRCm39) |
D336E |
probably benign |
Het |
| Fcsk |
G |
T |
8: 111,613,891 (GRCm39) |
D723E |
probably damaging |
Het |
| Fras1 |
T |
C |
5: 96,793,829 (GRCm39) |
|
probably null |
Het |
| Garem1 |
T |
A |
18: 21,281,947 (GRCm39) |
E136D |
probably damaging |
Het |
| Haus6 |
A |
G |
4: 86,521,104 (GRCm39) |
I178T |
probably benign |
Het |
| Igkv3-2 |
T |
G |
6: 70,675,480 (GRCm39) |
V10G |
possibly damaging |
Het |
| Jrkl |
A |
C |
9: 13,244,236 (GRCm39) |
I475R |
possibly damaging |
Het |
| Lcmt1 |
C |
T |
7: 123,003,683 (GRCm39) |
H146Y |
probably damaging |
Het |
| Lipk |
A |
G |
19: 34,017,829 (GRCm39) |
N289S |
probably damaging |
Het |
| Mb |
A |
G |
15: 76,901,789 (GRCm39) |
V102A |
probably benign |
Het |
| Mc4r |
T |
A |
18: 66,992,892 (GRCm39) |
N74Y |
probably damaging |
Het |
| Mink1 |
G |
T |
11: 70,499,776 (GRCm39) |
R773L |
possibly damaging |
Het |
| Mroh2b |
A |
G |
15: 4,973,131 (GRCm39) |
I1045V |
probably benign |
Het |
| Myo15a |
A |
T |
11: 60,370,057 (GRCm39) |
E939V |
possibly damaging |
Het |
| Ndufs7 |
T |
C |
10: 80,088,255 (GRCm39) |
I14T |
probably benign |
Het |
| Nlrp4b |
T |
C |
7: 10,448,808 (GRCm39) |
V337A |
probably benign |
Het |
| Npm2 |
T |
C |
14: 70,890,060 (GRCm39) |
|
probably null |
Het |
| Or10ab4 |
T |
C |
7: 107,654,642 (GRCm39) |
F151S |
probably damaging |
Het |
| Or2h2c |
A |
G |
17: 37,422,227 (GRCm39) |
Y216H |
probably damaging |
Het |
| Or4a68 |
G |
A |
2: 89,269,727 (GRCm39) |
L299F |
probably damaging |
Het |
| Prkch |
C |
T |
12: 73,822,290 (GRCm39) |
P630S |
probably damaging |
Het |
| Ptprn |
T |
C |
1: 75,229,411 (GRCm39) |
|
probably null |
Het |
| Rnf31 |
T |
A |
14: 55,840,851 (GRCm39) |
D884E |
probably damaging |
Het |
| Semp2l2a |
T |
G |
8: 13,886,736 (GRCm39) |
I452L |
probably benign |
Het |
| Slc22a27 |
A |
T |
19: 7,903,815 (GRCm39) |
N107K |
possibly damaging |
Het |
| Tln1 |
G |
T |
4: 43,540,597 (GRCm39) |
A1468D |
probably damaging |
Het |
| Tmem185b |
T |
A |
1: 119,454,781 (GRCm39) |
F181I |
possibly damaging |
Het |
| Tmem63a |
G |
A |
1: 180,790,679 (GRCm39) |
D446N |
possibly damaging |
Het |
| Trappc11 |
T |
C |
8: 47,958,351 (GRCm39) |
|
probably benign |
Het |
| Vmn1r218 |
A |
T |
13: 23,321,081 (GRCm39) |
N63Y |
probably damaging |
Het |
| Vps37c |
A |
G |
19: 10,683,632 (GRCm39) |
D18G |
probably damaging |
Het |
|
| Other mutations in Prdm9 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH 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 |
|
|
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 |
|
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'- CAGCTTAGACAAGACCAAGTTC -3'
(R):5'- AGAAAGCCTAGCAGATGGCC -3'
Sequencing Primer
(F):5'- GCTTAGACAAGACCAAGTTCAGAAC -3'
(R):5'- AAAGCCTAGCAGATGGCCTCTTG -3'
|
| Posted On |
2015-01-23 |
Incidental Mutation