Incidental Mutation 'R4742:Prdm9'
| ID |
358154 |
| 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 |
041966-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.297)
|
| Stock # |
R4742 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
17 |
| Chromosomal Location |
15763341-15784616 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 15773783 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glutamic Acid
at position 329
(D329E)
|
| 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 |
probably benign
Transcript: ENSMUST00000147532
AA Change: D204E
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000118454
Gene: ENSMUSG00000051977
AA Change: D204E
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SSXRD
|
49 |
81 |
1.8e-19 |
PFAM |
|
SET
|
123 |
243 |
2.56e-2 |
SMART |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000167994
AA Change: D329E
PolyPhen 2
Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000131871
Gene: ENSMUSG00000051977
AA Change: D329E
| 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 |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000231919
|
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.5%
- 10x: 96.8%
- 20x: 93.9%
|
| Validation Efficiency |
94% (51/54) |
| 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: 47 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 8030423J24Rik |
G |
T |
13: 71,031,644 (GRCm39) |
R17L |
unknown |
Het |
| Acan |
T |
C |
7: 78,750,517 (GRCm39) |
F1763L |
probably benign |
Het |
| Adgrb1 |
T |
A |
15: 74,401,328 (GRCm39) |
L108* |
probably null |
Het |
| Anapc2 |
T |
A |
2: 25,163,555 (GRCm39) |
|
probably null |
Het |
| Apbb1ip |
A |
G |
2: 22,716,928 (GRCm39) |
K177E |
unknown |
Het |
| Azgp1 |
T |
A |
5: 137,987,888 (GRCm39) |
Y223* |
probably null |
Het |
| Cfap44 |
T |
G |
16: 44,269,615 (GRCm39) |
|
probably null |
Het |
| Chfr |
C |
T |
5: 110,291,464 (GRCm39) |
T94I |
probably benign |
Het |
| Chrna10 |
T |
G |
7: 101,762,344 (GRCm39) |
Q282P |
probably damaging |
Het |
| Col9a3 |
G |
T |
2: 180,245,180 (GRCm39) |
G130W |
unknown |
Het |
| Dcaf1 |
A |
G |
9: 106,735,754 (GRCm39) |
T901A |
probably benign |
Het |
| Dock2 |
T |
G |
11: 34,244,170 (GRCm39) |
|
probably null |
Het |
| Dysf |
C |
A |
6: 84,074,697 (GRCm39) |
D499E |
probably damaging |
Het |
| Fdxacb1 |
A |
G |
9: 50,679,968 (GRCm39) |
|
probably benign |
Het |
| Fhip1b |
A |
G |
7: 105,033,518 (GRCm39) |
V566A |
probably damaging |
Het |
| Il31ra |
G |
T |
13: 112,660,501 (GRCm39) |
S615* |
probably null |
Het |
| Itgam |
C |
T |
7: 127,712,245 (GRCm39) |
S827F |
probably damaging |
Het |
| Mapkbp1 |
T |
A |
2: 119,847,299 (GRCm39) |
V512E |
probably damaging |
Het |
| Myo1c |
C |
T |
11: 75,560,856 (GRCm39) |
R770* |
probably null |
Het |
| Nab2 |
T |
C |
10: 127,498,696 (GRCm39) |
T458A |
probably benign |
Het |
| Nadsyn1 |
A |
G |
7: 143,352,367 (GRCm39) |
|
probably benign |
Het |
| Nek10 |
A |
G |
14: 14,861,624 (GRCm38) |
D560G |
probably null |
Het |
| Or2ag13 |
A |
T |
7: 106,472,635 (GRCm39) |
N272K |
probably damaging |
Het |
| Or2ak6 |
A |
G |
11: 58,592,685 (GRCm39) |
R53G |
probably benign |
Het |
| Or8b46 |
T |
C |
9: 38,450,952 (GRCm39) |
S254P |
probably damaging |
Het |
| Pou1f1 |
C |
A |
16: 65,320,367 (GRCm39) |
P19T |
probably benign |
Het |
| Prkn |
T |
A |
17: 11,456,591 (GRCm39) |
|
probably null |
Het |
| Ptprm |
A |
C |
17: 67,051,746 (GRCm39) |
Y962* |
probably null |
Het |
| Rad9a |
G |
A |
19: 4,250,560 (GRCm39) |
R85C |
probably damaging |
Het |
| Rhox2c |
A |
C |
X: 36,635,351 (GRCm39) |
Q4H |
probably benign |
Het |
| Rlig1 |
T |
C |
10: 100,414,243 (GRCm39) |
I139V |
probably benign |
Het |
| Rtkn2 |
A |
G |
10: 67,839,144 (GRCm39) |
T154A |
possibly damaging |
Het |
| Slitrk3 |
T |
C |
3: 72,955,898 (GRCm39) |
D958G |
probably benign |
Het |
| Spata31d1b |
C |
A |
13: 59,864,426 (GRCm39) |
H525N |
probably damaging |
Het |
| Tacc2 |
A |
G |
7: 130,227,697 (GRCm39) |
R1461G |
probably benign |
Het |
| Tas2r105 |
G |
A |
6: 131,663,814 (GRCm39) |
H205Y |
probably damaging |
Het |
| Tenm4 |
A |
G |
7: 96,446,691 (GRCm39) |
N809D |
probably damaging |
Het |
| Thoc2l |
A |
T |
5: 104,666,723 (GRCm39) |
N415I |
probably benign |
Het |
| Tns1 |
A |
G |
1: 74,163,449 (GRCm39) |
|
probably null |
Het |
| Top1 |
A |
G |
2: 160,545,490 (GRCm39) |
|
probably null |
Het |
| Traf3ip2 |
C |
T |
10: 39,515,256 (GRCm39) |
P345S |
possibly damaging |
Het |
| Ttn |
T |
A |
2: 76,585,168 (GRCm39) |
I22042F |
probably damaging |
Het |
| Txndc9 |
T |
C |
1: 38,026,765 (GRCm39) |
D135G |
possibly damaging |
Het |
| Usp3 |
A |
G |
9: 66,427,959 (GRCm39) |
Y339H |
probably damaging |
Het |
| Vmn1r5 |
A |
T |
6: 56,963,236 (GRCm39) |
K304* |
probably null |
Het |
| Vmn2r92 |
A |
G |
17: 18,387,119 (GRCm39) |
T153A |
probably benign |
Het |
| Xkr5 |
A |
T |
8: 18,998,746 (GRCm39) |
*55K |
probably null |
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 |
|
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'- AATCATAATAGTGCCCACCTCTTCC -3'
(R):5'- TGAAAACTGGGCTCTTGGGG -3'
Sequencing Primer
(F):5'- ACCTCTTCCTGCTGTGAATC -3'
(R):5'- CTTGGAGCTAGGATATCCGTAAC -3'
|
| Posted On |
2015-11-11 |
Incidental Mutation