Incidental Mutation 'R7875:Prdm9'
| ID |
608408 |
| 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 |
045927-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.297)
|
| Stock # |
R7875 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
17 |
| Chromosomal Location |
15763341-15784616 bp(-) (GRCm39) |
| Type of Mutation |
nonsense |
| DNA Base Change (assembly) |
A to T
at 15773804 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Stop codon
at position 322
(Y322*)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000131871
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000147532]
[ENSMUST00000167994]
|
| AlphaFold |
Q96EQ9 |
| Predicted Effect |
probably null
Transcript: ENSMUST00000147532
AA Change: Y197*
|
| SMART Domains |
Protein: ENSMUSP00000118454
Gene: ENSMUSG00000051977
AA Change: Y197*
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SSXRD
|
49 |
81 |
1.8e-19 |
PFAM |
|
SET
|
123 |
243 |
2.56e-2 |
SMART |
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000167994
AA Change: Y322*
|
| SMART Domains |
Protein: ENSMUSP00000131871
Gene: ENSMUSG00000051977
AA Change: Y322*
| 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: 100.0%
- 3x: 100.0%
- 10x: 99.7%
- 20x: 99.2%
|
| Validation Efficiency |
|
| 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 |
|---|
| Acap2 |
A |
T |
16: 30,958,459 (GRCm39) |
F102I |
probably damaging |
Het |
| Acp7 |
A |
T |
7: 28,314,152 (GRCm39) |
Y348N |
probably damaging |
Het |
| Adgre4 |
A |
T |
17: 56,099,016 (GRCm39) |
D174V |
probably benign |
Het |
| Ahdc1 |
A |
G |
4: 132,791,161 (GRCm39) |
T801A |
possibly damaging |
Het |
| Aldh1a7 |
A |
C |
19: 20,693,343 (GRCm39) |
V192G |
possibly damaging |
Het |
| Anp32b |
T |
G |
4: 46,451,301 (GRCm39) |
D2E |
probably benign |
Het |
| Arhgef11 |
A |
T |
3: 87,591,808 (GRCm39) |
D53V |
probably damaging |
Het |
| Arid5b |
T |
C |
10: 67,964,771 (GRCm39) |
N300S |
probably benign |
Het |
| Ascc2 |
A |
G |
11: 4,618,389 (GRCm39) |
N328S |
probably benign |
Het |
| Aspm |
A |
T |
1: 139,382,872 (GRCm39) |
Q68L |
probably benign |
Het |
| Ccng2 |
C |
G |
5: 93,421,202 (GRCm39) |
S237R |
probably benign |
Het |
| Ccser1 |
A |
T |
6: 61,288,932 (GRCm39) |
H365L |
probably benign |
Het |
| Col1a2 |
T |
A |
6: 4,518,500 (GRCm39) |
N213K |
unknown |
Het |
| Col7a1 |
T |
C |
9: 108,787,763 (GRCm39) |
V681A |
unknown |
Het |
| Cplane1 |
A |
G |
15: 8,239,446 (GRCm39) |
I1216V |
probably benign |
Het |
| Dock9 |
A |
T |
14: 121,863,396 (GRCm39) |
Y792* |
probably null |
Het |
| Fam241b |
A |
T |
10: 61,970,271 (GRCm39) |
S10R |
|
Het |
| Gab1 |
C |
T |
8: 81,515,395 (GRCm39) |
D308N |
probably damaging |
Het |
| Gdf11 |
C |
T |
10: 128,722,210 (GRCm39) |
R215H |
probably benign |
Het |
| Gpc1 |
T |
C |
1: 92,782,970 (GRCm39) |
|
probably null |
Het |
| Hnf4a |
G |
T |
2: 163,400,980 (GRCm39) |
E200* |
probably null |
Het |
| Ints2 |
T |
C |
11: 86,103,888 (GRCm39) |
T1086A |
probably damaging |
Het |
| Kbtbd7 |
A |
G |
14: 79,664,806 (GRCm39) |
T213A |
probably benign |
Het |
| Kcnt2 |
A |
G |
1: 140,501,385 (GRCm39) |
D917G |
probably damaging |
Het |
| Kdm5a |
C |
A |
6: 120,375,979 (GRCm39) |
Y578* |
probably null |
Het |
| Lrrtm4 |
A |
T |
6: 79,999,343 (GRCm39) |
T252S |
possibly damaging |
Het |
| Mamdc4 |
C |
T |
2: 25,458,677 (GRCm39) |
W305* |
probably null |
Het |
| Mzb1 |
A |
G |
18: 35,780,913 (GRCm39) |
I125T |
possibly damaging |
Het |
| Nfrkb |
A |
G |
9: 31,321,450 (GRCm39) |
T716A |
possibly damaging |
Het |
| Or2ad1 |
T |
A |
13: 21,327,093 (GRCm39) |
I45F |
probably damaging |
Het |
| Or4f6 |
A |
G |
2: 111,839,192 (GRCm39) |
V113A |
probably benign |
Het |
| Or52r1b |
A |
G |
7: 102,691,060 (GRCm39) |
M120V |
probably damaging |
Het |
| Or8k16 |
G |
A |
2: 85,519,838 (GRCm39) |
E22K |
probably benign |
Het |
| Plcxd2 |
G |
A |
16: 45,830,065 (GRCm39) |
A52V |
possibly damaging |
Het |
| Poteg |
C |
T |
8: 27,939,942 (GRCm39) |
P95L |
probably benign |
Het |
| Rab11fip2 |
G |
C |
19: 59,925,655 (GRCm39) |
I187M |
possibly damaging |
Het |
| Ranbp2 |
G |
T |
10: 58,314,277 (GRCm39) |
E1666* |
probably null |
Het |
| Rin3 |
T |
C |
12: 102,335,735 (GRCm39) |
S549P |
probably damaging |
Het |
| Scn10a |
C |
T |
9: 119,464,508 (GRCm39) |
|
probably null |
Het |
| Scn3a |
A |
G |
2: 65,327,826 (GRCm39) |
F888S |
probably damaging |
Het |
| Sik3 |
T |
A |
9: 46,034,528 (GRCm39) |
I96N |
probably damaging |
Het |
| Slc12a7 |
T |
A |
13: 73,936,723 (GRCm39) |
C128S |
possibly damaging |
Het |
| Spata31h1 |
T |
C |
10: 82,123,456 (GRCm39) |
S3185G |
possibly damaging |
Het |
| Syde2 |
A |
G |
3: 145,726,020 (GRCm39) |
E1304G |
probably damaging |
Het |
| Tagln |
T |
C |
9: 45,841,680 (GRCm39) |
I199V |
probably damaging |
Het |
| Tars3 |
T |
A |
7: 65,327,899 (GRCm39) |
V536E |
probably benign |
Het |
| Tas2r140 |
A |
G |
6: 40,469,097 (GRCm39) |
K309R |
probably damaging |
Het |
| Thra |
A |
T |
11: 98,659,257 (GRCm39) |
D462V |
probably damaging |
Het |
| Topaz1 |
A |
G |
9: 122,578,652 (GRCm39) |
T521A |
possibly damaging |
Het |
| Uhrf1 |
A |
G |
17: 56,619,884 (GRCm39) |
N265S |
possibly damaging |
Het |
| Upk3b |
A |
T |
5: 136,069,057 (GRCm39) |
Y142F |
probably benign |
Het |
| Vmn1r219 |
T |
C |
13: 23,347,363 (GRCm39) |
V184A |
possibly damaging |
Het |
| Vmn1r58 |
T |
C |
7: 5,413,753 (GRCm39) |
D159G |
probably damaging |
Het |
| Vnn3 |
C |
A |
10: 23,743,146 (GRCm39) |
A452D |
possibly damaging |
Het |
| Wscd1 |
T |
A |
11: 71,679,560 (GRCm39) |
Y478N |
probably damaging |
Het |
| Xrcc5 |
C |
T |
1: 72,369,090 (GRCm39) |
R315C |
probably damaging |
Het |
| Zkscan5 |
A |
C |
5: 145,157,676 (GRCm39) |
H726P |
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 |
|
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 |
|
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'- GGAATCATAATAGTGCCCACCTC -3'
(R):5'- TGAAAACTGGGCTCTTGGGG -3'
Sequencing Primer
(F):5'- ATAATAGTGCCCACCTCTTCCTG -3'
(R):5'- CCTTTGGGATAGATGAACAGGGC -3'
|
| Posted On |
2019-12-20 |
Incidental Mutation