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)
|
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
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: 99.9%
- 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
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
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 |
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 |
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 |