Incidental Mutation 'R7041:Prdm9'
| ID |
547080 |
| 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 |
045140-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.351)
|
| Stock # |
R7041 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
17 |
| Chromosomal Location |
15763341-15784616 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to A
at 15765257 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Alanine to Serine
at position 508
(A508S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000131871
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000167994]
|
| AlphaFold |
Q96EQ9 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000167994
AA Change: A508S
PolyPhen 2
Score 0.565 (Sensitivity: 0.88; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000131871
Gene: ENSMUSG00000051977
AA Change: A508S
| 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: 100.0%
- 3x: 100.0%
- 10x: 99.8%
- 20x: 99.3%
|
| Validation Efficiency |
96% (53/55) |
| 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: 54 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acan |
G |
T |
7: 78,748,096 (GRCm39) |
E956* |
probably null |
Het |
| Adam25 |
A |
T |
8: 41,207,121 (GRCm39) |
H129L |
probably benign |
Het |
| Adgrl4 |
A |
T |
3: 151,144,959 (GRCm39) |
H36L |
probably benign |
Het |
| Ago1 |
T |
A |
4: 126,357,499 (GRCm39) |
I59F |
possibly damaging |
Het |
| Anapc1 |
A |
T |
2: 128,470,576 (GRCm39) |
V1518E |
possibly damaging |
Het |
| Atxn1 |
A |
G |
13: 45,720,311 (GRCm39) |
I528T |
probably damaging |
Het |
| B4galnt4 |
A |
G |
7: 140,650,593 (GRCm39) |
H820R |
probably damaging |
Het |
| Cacna1h |
T |
C |
17: 25,612,977 (GRCm39) |
E282G |
probably damaging |
Het |
| Camk1 |
T |
A |
6: 113,316,475 (GRCm39) |
M95L |
probably benign |
Het |
| Capn7 |
C |
T |
14: 31,058,642 (GRCm39) |
|
probably benign |
Het |
| Cav1 |
A |
G |
6: 17,339,143 (GRCm39) |
E45G |
possibly damaging |
Het |
| Ccdc183 |
T |
G |
2: 25,503,682 (GRCm39) |
E185A |
probably benign |
Het |
| Ccl2 |
T |
A |
11: 81,926,489 (GRCm39) |
M1K |
probably null |
Het |
| Cep97 |
T |
A |
16: 55,726,117 (GRCm39) |
H590L |
probably benign |
Het |
| Dsg1c |
A |
T |
18: 20,399,201 (GRCm39) |
I102F |
probably damaging |
Het |
| Fcho2 |
A |
G |
13: 98,921,334 (GRCm39) |
Y184H |
possibly damaging |
Het |
| Gart |
C |
T |
16: 91,440,031 (GRCm39) |
|
probably benign |
Het |
| Gask1a |
A |
T |
9: 121,794,467 (GRCm39) |
Q207L |
probably damaging |
Het |
| Golga3 |
G |
A |
5: 110,356,450 (GRCm39) |
|
probably null |
Het |
| Hint3 |
G |
T |
10: 30,486,380 (GRCm39) |
A133E |
probably damaging |
Het |
| Hspe1 |
T |
C |
1: 55,128,376 (GRCm39) |
|
probably null |
Het |
| Insr |
A |
T |
8: 3,308,418 (GRCm39) |
V206E |
probably benign |
Het |
| Insrr |
T |
C |
3: 87,722,551 (GRCm39) |
S1258P |
probably damaging |
Het |
| Itga11 |
C |
T |
9: 62,659,538 (GRCm39) |
T430M |
probably damaging |
Het |
| Jmjd1c |
G |
A |
10: 67,056,388 (GRCm39) |
V890I |
possibly damaging |
Het |
| Kdm4b |
T |
A |
17: 56,703,592 (GRCm39) |
S717R |
probably damaging |
Het |
| Large1 |
A |
T |
8: 73,843,092 (GRCm39) |
C144S |
probably damaging |
Het |
| Lrat |
G |
T |
3: 82,810,755 (GRCm39) |
Q89K |
probably benign |
Het |
| Lrrc66 |
A |
T |
5: 73,765,899 (GRCm39) |
F381L |
possibly damaging |
Het |
| Myo15a |
A |
G |
11: 60,396,832 (GRCm39) |
T2634A |
probably damaging |
Het |
| Nup205 |
T |
G |
6: 35,201,470 (GRCm39) |
I1182M |
possibly damaging |
Het |
| Or2a51 |
T |
A |
6: 43,178,837 (GRCm39) |
D86E |
probably benign |
Het |
| Or5m10 |
A |
T |
2: 85,717,965 (GRCm39) |
I274F |
probably benign |
Het |
| Or6c66 |
T |
A |
10: 129,461,603 (GRCm39) |
E109V |
probably damaging |
Het |
| Plekha6 |
T |
A |
1: 133,200,198 (GRCm39) |
V259D |
possibly damaging |
Het |
| Prickle2 |
A |
G |
6: 92,353,286 (GRCm39) |
F783L |
probably benign |
Het |
| Ptprc |
T |
C |
1: 138,054,047 (GRCm39) |
S31G |
probably benign |
Het |
| Rbak |
A |
T |
5: 143,159,226 (GRCm39) |
I609N |
probably damaging |
Het |
| Rimklb |
A |
T |
6: 122,436,176 (GRCm39) |
L134* |
probably null |
Het |
| Ripor2 |
A |
G |
13: 24,877,749 (GRCm39) |
I250V |
probably benign |
Het |
| Sorbs1 |
G |
C |
19: 40,365,244 (GRCm39) |
R180G |
probably benign |
Het |
| Spaca6 |
C |
T |
17: 18,056,358 (GRCm39) |
L118F |
probably benign |
Het |
| Tmem167 |
G |
A |
13: 90,246,533 (GRCm39) |
C19Y |
probably benign |
Het |
| Togaram1 |
C |
T |
12: 65,067,160 (GRCm39) |
T1684I |
possibly damaging |
Het |
| Trappc8 |
T |
C |
18: 21,007,729 (GRCm39) |
T129A |
probably benign |
Het |
| Ubash3a |
A |
G |
17: 31,447,184 (GRCm39) |
S347G |
probably benign |
Het |
| Unc80 |
T |
C |
1: 66,542,752 (GRCm39) |
S289P |
probably benign |
Het |
| Vmn2r11 |
A |
G |
5: 109,202,816 (GRCm39) |
I87T |
probably damaging |
Het |
| Vmn2r54 |
A |
T |
7: 12,363,751 (GRCm39) |
F381I |
probably damaging |
Het |
| Wdsub1 |
A |
G |
2: 59,683,224 (GRCm39) |
L450P |
probably damaging |
Het |
| Xylt2 |
A |
G |
11: 94,558,408 (GRCm39) |
|
probably null |
Het |
| Zfp429 |
A |
T |
13: 67,538,830 (GRCm39) |
C205S |
probably damaging |
Het |
| Zfp60 |
T |
C |
7: 27,448,451 (GRCm39) |
I373T |
probably benign |
Het |
| Zfp738 |
A |
G |
13: 67,818,420 (GRCm39) |
S524P |
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 |
|
|
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 |
|
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'- TGCAAACATAGGGCTTCTCC -3'
(R):5'- AGCTTCAGGAACAACATGTTG -3'
Sequencing Primer
(F):5'- GGCTTCTCCCCTGTGTGTG -3'
(R):5'- GCTTCAGGAACAACATGTTGATTCAC -3'
|
| Posted On |
2019-05-13 |
Incidental Mutation