Incidental Mutation 'R5130:Prdm9'
ID |
394976 |
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 |
042718-MU
|
Accession Numbers |
|
Essential gene? |
Possibly non essential
(E-score: 0.351)
|
Stock # |
R5130 (G1)
|
Quality Score |
93 |
Status
|
Validated
|
Chromosome |
17 |
Chromosomal Location |
15763341-15784616 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to C
at 15764729 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Arginine to Glycine
at position 684
(R684G)
|
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: R684G
PolyPhen 2
Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
|
SMART Domains |
Protein: ENSMUSP00000131871 Gene: ENSMUSG00000051977 AA Change: R684G
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
|
Meta Mutation Damage Score |
0.1415 |
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 96.7%
- 20x: 93.4%
|
Validation Efficiency |
96% (51/53) |
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: 45 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
4930558K02Rik |
T |
C |
1: 161,780,184 (GRCm39) |
N110S |
possibly damaging |
Het |
Acss3 |
T |
C |
10: 106,840,586 (GRCm39) |
I392V |
possibly damaging |
Het |
Agbl5 |
G |
A |
5: 31,060,403 (GRCm39) |
R141Q |
probably damaging |
Het |
Arhgef11 |
A |
G |
3: 87,633,321 (GRCm39) |
H696R |
possibly damaging |
Het |
Baiap3 |
G |
T |
17: 25,464,316 (GRCm39) |
D847E |
probably benign |
Het |
Cdc27 |
T |
C |
11: 104,425,600 (GRCm39) |
K72R |
probably benign |
Het |
Cry2 |
T |
C |
2: 92,254,944 (GRCm39) |
E137G |
probably benign |
Het |
Dhodh |
A |
T |
8: 110,322,388 (GRCm39) |
L237Q |
possibly damaging |
Het |
Dscam |
A |
T |
16: 96,620,979 (GRCm39) |
N576K |
probably benign |
Het |
Eng |
A |
G |
2: 32,571,518 (GRCm39) |
N636S |
probably damaging |
Het |
Ephx2 |
A |
T |
14: 66,345,511 (GRCm39) |
I151K |
probably damaging |
Het |
Fahd1 |
A |
G |
17: 25,068,733 (GRCm39) |
C115R |
probably damaging |
Het |
Fer1l4 |
T |
A |
2: 155,891,386 (GRCm39) |
I143F |
possibly damaging |
Het |
Iqgap3 |
C |
A |
3: 88,016,161 (GRCm39) |
N981K |
probably damaging |
Het |
Kcna5 |
T |
C |
6: 126,511,496 (GRCm39) |
I211V |
probably benign |
Het |
Mcm9 |
A |
T |
10: 53,506,495 (GRCm39) |
V14E |
possibly damaging |
Het |
Mlh1 |
A |
G |
9: 111,058,906 (GRCm39) |
|
probably null |
Het |
Mylk |
A |
G |
16: 34,809,367 (GRCm39) |
K1775E |
probably damaging |
Het |
Myo18b |
T |
C |
5: 113,021,769 (GRCm39) |
D541G |
probably benign |
Het |
Ncapd2 |
A |
T |
6: 125,146,887 (GRCm39) |
M1233K |
possibly damaging |
Het |
Nf2 |
A |
T |
11: 4,779,862 (GRCm39) |
|
probably benign |
Het |
Nova2 |
C |
T |
7: 18,660,069 (GRCm39) |
T22I |
unknown |
Het |
Or3a1d |
A |
T |
11: 74,237,993 (GRCm39) |
M19K |
probably damaging |
Het |
Or7g28 |
T |
A |
9: 19,272,369 (GRCm39) |
Y94F |
possibly damaging |
Het |
Or8b12 |
T |
A |
9: 37,657,805 (GRCm39) |
I125N |
probably damaging |
Het |
Pcdha2 |
A |
T |
18: 37,073,722 (GRCm39) |
N451I |
probably damaging |
Het |
Pcdhb12 |
T |
A |
18: 37,568,877 (GRCm39) |
F8I |
probably benign |
Het |
Pdzph1 |
A |
C |
17: 59,229,604 (GRCm39) |
L1018W |
probably damaging |
Het |
Rabep1 |
T |
A |
11: 70,795,557 (GRCm39) |
V261E |
probably damaging |
Het |
Ros1 |
T |
A |
10: 52,040,037 (GRCm39) |
Y318F |
possibly damaging |
Het |
Samd9l |
A |
T |
6: 3,374,548 (GRCm39) |
D904E |
possibly damaging |
Het |
Siah3 |
A |
T |
14: 75,763,381 (GRCm39) |
K211* |
probably null |
Het |
Slc5a8 |
T |
A |
10: 88,762,077 (GRCm39) |
N572K |
probably benign |
Het |
Slfn8 |
A |
G |
11: 82,894,647 (GRCm39) |
F664S |
probably benign |
Het |
Sowahb |
T |
A |
5: 93,190,630 (GRCm39) |
K696N |
possibly damaging |
Het |
St7l |
A |
T |
3: 104,803,080 (GRCm39) |
H330L |
probably damaging |
Het |
Tnrc6c |
T |
A |
11: 117,629,176 (GRCm39) |
|
probably null |
Het |
Ttc28 |
G |
T |
5: 111,040,722 (GRCm39) |
V37F |
probably benign |
Het |
Uaca |
C |
A |
9: 60,787,510 (GRCm39) |
Q1409K |
probably damaging |
Het |
V1rd19 |
T |
A |
7: 23,702,537 (GRCm39) |
M1K |
probably null |
Het |
Vmn1r225 |
A |
G |
17: 20,723,047 (GRCm39) |
R163G |
possibly damaging |
Het |
Wdr87-ps |
T |
C |
7: 29,228,699 (GRCm39) |
|
noncoding transcript |
Het |
Zc3h3 |
C |
A |
15: 75,651,139 (GRCm39) |
V694L |
probably damaging |
Het |
Zfp442 |
G |
T |
2: 150,251,530 (GRCm39) |
T123K |
possibly damaging |
Het |
Zmym1 |
A |
T |
4: 126,942,451 (GRCm39) |
S646T |
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 |
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'- TGCAAACATAGGGCTTCTCC -3'
(R):5'- GGGCTTTACACAGAAGTCAGAC -3'
Sequencing Primer
(F):5'- GGCTTCTCCCCTGTGTGTG -3'
(R):5'- AGAAGCCCTATGTTTGCAGG -3'
|
Posted On |
2016-06-21 |