Incidental Mutation 'R4118:Prdm9'
| ID |
315196 |
| 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 |
041631-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.297)
|
| Stock # |
R4118 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
17 |
| Chromosomal Location |
15763341-15784616 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to G
at 15764275 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Alanine
at position 835
(D835A)
|
| 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: D835A
PolyPhen 2
Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)
|
| SMART Domains |
Protein: ENSMUSP00000131871
Gene: ENSMUSG00000051977
AA Change: D835A
| 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 |
0.0898 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.4%
- 20x: 95.7%
|
| Validation Efficiency |
92% (55/60) |
| 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 |
|---|
| 1700003H04Rik |
T |
C |
3: 124,373,503 (GRCm39) |
R31G |
possibly damaging |
Het |
| 4932414N04Rik |
C |
T |
2: 68,566,857 (GRCm39) |
R419C |
probably benign |
Het |
| Ankmy1 |
T |
C |
1: 92,816,418 (GRCm39) |
E232G |
possibly damaging |
Het |
| Arhgef4 |
A |
T |
1: 34,771,428 (GRCm39) |
K1245M |
probably damaging |
Het |
| Atp2c1 |
A |
G |
9: 105,343,858 (GRCm39) |
L83P |
probably damaging |
Het |
| Atp9b |
T |
C |
18: 80,793,044 (GRCm39) |
D1000G |
possibly damaging |
Het |
| Atxn7 |
T |
C |
14: 14,100,308 (GRCm38) |
S665P |
probably benign |
Het |
| Bbs4 |
T |
C |
9: 59,237,708 (GRCm39) |
Y212C |
possibly damaging |
Het |
| Cars1 |
A |
G |
7: 143,113,384 (GRCm39) |
|
probably null |
Het |
| Cep162 |
T |
C |
9: 87,086,229 (GRCm39) |
T1032A |
probably benign |
Het |
| Chd7 |
G |
A |
4: 8,865,831 (GRCm39) |
E668K |
probably damaging |
Het |
| Dek |
T |
C |
13: 47,242,076 (GRCm39) |
T201A |
probably benign |
Het |
| Depdc5 |
T |
A |
5: 33,121,979 (GRCm39) |
S1079T |
probably damaging |
Het |
| Etaa1 |
A |
T |
11: 17,896,180 (GRCm39) |
S646T |
probably benign |
Het |
| Fat1 |
T |
C |
8: 45,463,474 (GRCm39) |
S1339P |
probably damaging |
Het |
| Fat1 |
C |
A |
8: 45,503,981 (GRCm39) |
D4491E |
probably damaging |
Het |
| Gmps |
T |
C |
3: 63,887,615 (GRCm39) |
V29A |
probably benign |
Het |
| Gpr18 |
T |
C |
14: 122,149,968 (GRCm39) |
E19G |
probably benign |
Het |
| Ipo5 |
A |
G |
14: 121,176,073 (GRCm39) |
T633A |
probably benign |
Het |
| Jmjd1c |
T |
A |
10: 67,055,532 (GRCm39) |
S317R |
probably damaging |
Het |
| Lama3 |
T |
A |
18: 12,583,488 (GRCm39) |
M692K |
probably benign |
Het |
| Lrp12 |
A |
T |
15: 39,741,361 (GRCm39) |
C451* |
probably null |
Het |
| Lrp2 |
C |
T |
2: 69,260,606 (GRCm39) |
|
probably null |
Het |
| Myrfl |
T |
A |
10: 116,664,870 (GRCm39) |
I387F |
probably damaging |
Het |
| Naglu |
G |
A |
11: 100,964,908 (GRCm39) |
V332I |
probably benign |
Het |
| Nat2 |
G |
A |
8: 67,954,271 (GRCm39) |
R127H |
possibly damaging |
Het |
| Otx2 |
G |
A |
14: 48,896,611 (GRCm39) |
T141I |
probably benign |
Het |
| Paqr9 |
T |
A |
9: 95,442,952 (GRCm39) |
I314N |
probably damaging |
Het |
| Pds5b |
CATTTATTTATTTATTTATTTATTTATTTATTTATTTAT |
CATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTAT |
5: 150,698,819 (GRCm39) |
|
probably benign |
Het |
| Ppm1d |
A |
G |
11: 85,202,408 (GRCm39) |
D37G |
probably benign |
Het |
| Ptprq |
A |
G |
10: 107,547,781 (GRCm39) |
S206P |
probably benign |
Het |
| Rapgef2 |
A |
G |
3: 78,976,194 (GRCm39) |
|
probably null |
Het |
| Rpgrip1l |
G |
A |
8: 91,979,535 (GRCm39) |
T969I |
probably benign |
Het |
| Rpp40 |
A |
G |
13: 36,080,787 (GRCm39) |
Y316H |
probably damaging |
Het |
| Serpinb3d |
A |
T |
1: 107,006,960 (GRCm39) |
D249E |
possibly damaging |
Het |
| Slc22a29 |
A |
C |
19: 8,137,893 (GRCm39) |
|
probably benign |
Het |
| Slc35f1 |
T |
C |
10: 52,965,464 (GRCm39) |
M293T |
probably damaging |
Het |
| Slmap |
A |
T |
14: 26,204,027 (GRCm39) |
L98H |
probably damaging |
Het |
| Tiam1 |
C |
T |
16: 89,673,921 (GRCm39) |
|
probably null |
Het |
| Tlr11 |
A |
G |
14: 50,600,684 (GRCm39) |
Y890C |
probably damaging |
Het |
| Tmem131l |
T |
C |
3: 83,868,074 (GRCm39) |
T194A |
probably benign |
Het |
| Ubap1 |
A |
T |
4: 41,371,767 (GRCm39) |
D26V |
probably damaging |
Het |
| Vmn2r91 |
T |
A |
17: 18,330,358 (GRCm39) |
N547K |
probably damaging |
Het |
| Wiz |
C |
T |
17: 32,588,331 (GRCm39) |
|
probably benign |
Het |
| Wwp2 |
A |
G |
8: 108,272,091 (GRCm39) |
T399A |
probably benign |
Het |
| Zfp729b |
A |
T |
13: 67,740,829 (GRCm39) |
F479I |
possibly damaging |
Het |
| Zswim5 |
G |
A |
4: 116,844,016 (GRCm39) |
R1018H |
possibly 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 |
|
|
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 |
|
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'- TTGAAAATGAGAATTTGTAGCCAGG -3'
(R):5'- TCCTCATCCAGCACCAGAGG -3'
Sequencing Primer
(F):5'- GCAACTCTGATTTTGAGGCCAAC -3'
(R):5'- CCAGAGGACACACACAGGG -3'
|
| Posted On |
2015-05-14 |
Incidental Mutation