Incidental Mutation 'R8222:Prdm9'
| ID |
636790 |
| 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 |
067640-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.297)
|
| Stock # |
R8222 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
17 |
| Chromosomal Location |
15763341-15784616 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 15765035 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Proline
at position 582
(S582P)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000131871
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000167994]
|
| AlphaFold |
Q96EQ9 |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000167994
AA Change: S582P
PolyPhen 2
Score 0.925 (Sensitivity: 0.81; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000131871
Gene: ENSMUSG00000051977
AA Change: S582P
| 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: 99.9%
- 3x: 99.9%
- 10x: 99.5%
- 20x: 98.6%
|
| Validation Efficiency |
100% (56/56) |
| 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: 57 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aldh18a1 |
C |
T |
19: 40,562,296 (GRCm39) |
V243I |
probably benign |
Het |
| Ankrd11 |
A |
T |
8: 123,622,347 (GRCm39) |
S481T |
probably damaging |
Het |
| Atg2b |
A |
G |
12: 105,618,475 (GRCm39) |
I859T |
possibly damaging |
Het |
| B4galt3 |
G |
A |
1: 171,100,253 (GRCm39) |
R141Q |
possibly damaging |
Het |
| Bace1 |
T |
C |
9: 45,768,491 (GRCm39) |
V262A |
probably damaging |
Het |
| BC106179 |
A |
T |
16: 23,043,055 (GRCm39) |
I47N |
noncoding transcript |
Het |
| Brpf1 |
C |
T |
6: 113,286,999 (GRCm39) |
P76S |
probably benign |
Het |
| Cdk1 |
A |
G |
10: 69,176,426 (GRCm39) |
V227A |
probably benign |
Het |
| Ceacam20 |
T |
C |
7: 19,705,618 (GRCm39) |
V203A |
probably benign |
Het |
| Cfap251 |
T |
A |
5: 123,440,486 (GRCm39) |
Y1091N |
probably damaging |
Het |
| Cma2 |
T |
C |
14: 56,210,727 (GRCm39) |
V194A |
probably benign |
Het |
| Cnnm4 |
A |
G |
1: 36,545,617 (GRCm39) |
D749G |
probably benign |
Het |
| Cyp11b2 |
T |
C |
15: 74,728,059 (GRCm39) |
T8A |
probably benign |
Het |
| Dlk2 |
A |
G |
17: 46,613,384 (GRCm39) |
H170R |
probably benign |
Het |
| Esyt1 |
C |
T |
10: 128,347,647 (GRCm39) |
R987Q |
possibly damaging |
Het |
| Ganc |
T |
C |
2: 120,276,933 (GRCm39) |
I665T |
probably damaging |
Het |
| Gas6 |
T |
C |
8: 13,520,276 (GRCm39) |
T471A |
probably benign |
Het |
| Grik2 |
A |
G |
10: 49,449,744 (GRCm39) |
F153L |
probably benign |
Het |
| Heatr5b |
A |
G |
17: 79,109,130 (GRCm39) |
V1043A |
possibly damaging |
Het |
| Ipo5 |
A |
G |
14: 121,157,414 (GRCm39) |
D84G |
probably benign |
Het |
| Irak4 |
T |
A |
15: 94,459,110 (GRCm39) |
|
probably null |
Het |
| Lrp4 |
T |
A |
2: 91,305,086 (GRCm39) |
C238S |
probably damaging |
Het |
| Mau2 |
A |
T |
8: 70,485,827 (GRCm39) |
|
probably null |
Het |
| Mdn1 |
T |
C |
4: 32,707,477 (GRCm39) |
F1589L |
probably benign |
Het |
| Mlxip |
T |
G |
5: 123,585,596 (GRCm39) |
S662A |
probably benign |
Het |
| Mn1 |
A |
T |
5: 111,566,546 (GRCm39) |
N172I |
probably damaging |
Het |
| Mup2 |
A |
C |
4: 60,138,454 (GRCm39) |
D79E |
probably benign |
Het |
| Nab2 |
C |
A |
10: 127,498,645 (GRCm39) |
V475L |
probably benign |
Het |
| Nlrp3 |
A |
G |
11: 59,439,614 (GRCm39) |
E397G |
probably damaging |
Het |
| Odf2l |
A |
G |
3: 144,833,799 (GRCm39) |
E153G |
probably damaging |
Het |
| Or13p10 |
T |
C |
4: 118,523,113 (GRCm39) |
L133P |
probably damaging |
Het |
| Or51f5 |
G |
T |
7: 102,424,099 (GRCm39) |
D123Y |
probably damaging |
Het |
| Or5d36 |
T |
A |
2: 87,901,381 (GRCm39) |
Y115F |
probably benign |
Het |
| Or5l13 |
T |
C |
2: 87,779,788 (GRCm39) |
N263S |
probably benign |
Het |
| Pkdrej |
T |
A |
15: 85,701,640 (GRCm39) |
H1432L |
probably benign |
Het |
| Plec |
C |
T |
15: 76,063,374 (GRCm39) |
R2232H |
possibly damaging |
Het |
| Polk |
T |
C |
13: 96,632,023 (GRCm39) |
M317V |
possibly damaging |
Het |
| Ppp4r3a |
A |
G |
12: 101,008,164 (GRCm39) |
S758P |
probably benign |
Het |
| Pramel26 |
A |
T |
4: 143,536,893 (GRCm39) |
D479E |
possibly damaging |
Het |
| R3hcc1l |
T |
A |
19: 42,564,616 (GRCm39) |
L643H |
probably damaging |
Het |
| Rassf8 |
G |
A |
6: 145,765,783 (GRCm39) |
V38M |
unknown |
Het |
| Reln |
G |
A |
5: 22,136,475 (GRCm39) |
Q2518* |
probably null |
Het |
| Sel1l3 |
A |
G |
5: 53,345,296 (GRCm39) |
|
probably null |
Het |
| Serpina3m |
A |
T |
12: 104,358,960 (GRCm39) |
D324V |
possibly damaging |
Het |
| Slc12a6 |
T |
A |
2: 112,169,870 (GRCm39) |
|
probably null |
Het |
| Slc25a3 |
A |
G |
10: 90,954,053 (GRCm39) |
W219R |
probably damaging |
Het |
| Sort1 |
T |
A |
3: 108,241,951 (GRCm39) |
V299E |
probably benign |
Het |
| Stx6 |
A |
G |
1: 155,073,889 (GRCm39) |
D233G |
possibly damaging |
Het |
| Tefm |
A |
G |
11: 80,031,230 (GRCm39) |
V2A |
|
Het |
| Tfdp2 |
T |
C |
9: 96,192,666 (GRCm39) |
S190P |
possibly damaging |
Het |
| Tmprss7 |
A |
T |
16: 45,478,461 (GRCm39) |
I755N |
probably damaging |
Het |
| Trpm8 |
A |
G |
1: 88,253,390 (GRCm39) |
|
probably null |
Het |
| Ube2q2l |
A |
G |
6: 136,377,882 (GRCm39) |
I316T |
probably damaging |
Het |
| Ugt2a2 |
A |
G |
5: 87,608,369 (GRCm39) |
L490P |
probably damaging |
Het |
| Utp20 |
A |
G |
10: 88,614,234 (GRCm39) |
L1240P |
probably damaging |
Het |
| Vmn1r159 |
G |
T |
7: 22,542,608 (GRCm39) |
Y141* |
probably null |
Het |
| Vmn2r56 |
T |
A |
7: 12,444,960 (GRCm39) |
Y431F |
probably benign |
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 |
|
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 |
|
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'- TGACTTCTGTGTAAAGCCCC -3'
(R):5'- GTCAAATGTCAATGAGCACCAG -3'
Sequencing Primer
(F):5'- TGCAAACATAGGGCTTCTCC -3'
(R):5'- TGTCAATGAGCACCAGAAGAC -3'
|
| Posted On |
2020-07-13 |
Incidental Mutation